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Nextflow pipeline executor

Skill a5c-ai/babysitter/library/specializations/domains/science/bioinformatics/skills/nextflow-pipeline-executor

Nextflow workflow management skill for reproducible bioinformatics pipelinesFrom its SKILL.md

Install
npx -y skills add a5c-ai/babysitter --skill nextflow-pipeline-executor

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

SKILL.md

1.4 KB, 163 tokens by cl100k_base, as published. Nobody here has run it

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

What ships with it

Read from the repository

Just SKILL.md. No reference files, no scripts.

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