Agent-Skills.md

Agent Skills: Nextflow Pipeline Executor Skill

Nextflow workflow management skill for reproducible bioinformatics pipelines

bioinformaticsID: a5c-ai/babysitter/nextflow-pipeline-executor

Repository

a5c-ai/babysitter
a5c-aiLicense: MIT
244

Install this agent skill to your local

pnpm dlx add-skill https://github.com/a5c-ai/babysitter/tree/HEAD/plugins/babysitter/skills/babysit/process/specializations/domains/science/bioinformatics/skills/nextflow-pipeline-executor

Skill Files

Browse the full folder contents for nextflow-pipeline-executor.

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plugins/babysitter/skills/babysit/process/specializations/domains/science/bioinformatics/skills/nextflow-pipeline-executor/SKILL.md

Skill Metadata

Name
nextflow-pipeline-executor
Description
Nextflow workflow management skill for reproducible bioinformatics pipelines

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