# Nextflow Pipelines Step 2 Select Pipeline

> Sub-skill of nextflow-pipelines: Step 2: Select Pipeline.

- Skill: `vamseeachanta/nextflow-pipelines-step-2-select-pipeline` (Agent Skill)
- Install (CLI): `npx skillmds@latest add vamseeachanta/nextflow-pipelines-step-2-select-pipeline`
- Raw SKILL.md: https://api.skillmd.com/api/skills/vamseeachanta/nextflow-pipelines-step-2-select-pipeline/raw
- Safety review: PASS (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: DevOps & Infra
- Author: vamseeachanta (https://skillmd.com/u/vamseeachanta)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/vamseeachanta/nextflow-pipelines-step-2-select-pipeline

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# Step 2: Select Pipeline

## Step 2: Select Pipeline


**DECISION POINT: Confirm with user before proceeding.**

| Data Type | Pipeline | Version | Goal |
|-----------|----------|---------|------|
| RNA-seq | `rnaseq` | 3.22.2 | Gene expression |
| WGS/WES | `sarek` | 3.7.1 | Variant calling |
| ATAC-seq | `atacseq` | 2.1.2 | Chromatin accessibility |

Auto-detect from data:
```bash
python scripts/detect_data_type.py /path/to/data
```

For pipeline-specific details:
- [references/pipelines/rnaseq.md](references/pipelines/rnaseq.md)
- [references/pipelines/sarek.md](references/pipelines/sarek.md)
- [references/pipelines/atacseq.md](references/pipelines/atacseq.md)

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