# Nextflow Pipelines Step 3 Run Test Profile

> Sub-skill of nextflow-pipelines: Step 3: Run Test Profile.

- Skill: `vamseeachanta/nextflow-pipelines-step-3-run-test-profile` (Agent Skill)
- Install (CLI): `npx skillmds@latest add vamseeachanta/nextflow-pipelines-step-3-run-test-profile`
- Raw SKILL.md: https://api.skillmd.com/api/skills/vamseeachanta/nextflow-pipelines-step-3-run-test-profile/raw
- Safety review: PASS (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Research & Search
- Author: vamseeachanta (https://skillmd.com/u/vamseeachanta)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/vamseeachanta/nextflow-pipelines-step-3-run-test-profile

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# Step 3: Run Test Profile

## Step 3: Run Test Profile


**Validates environment with small data. MUST pass before real data.**

```bash
nextflow run nf-core/<pipeline> -r <version> -profile test,docker --outdir test_output
```

| Pipeline | Command |
|----------|---------|
| rnaseq | `nextflow run nf-core/rnaseq -r 3.22.2 -profile test,docker --outdir test_rnaseq` |
| sarek | `nextflow run nf-core/sarek -r 3.7.1 -profile test,docker --outdir test_sarek` |
| atacseq | `nextflow run nf-core/atacseq -r 2.1.2 -profile test,docker --outdir test_atacseq` |

Verify:
```bash
ls test_output/multiqc/multiqc_report.html
grep "Pipeline completed successfully" .nextflow.log
```

If test fails, see [references/troubleshooting.md](references/troubleshooting.md).

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