Sub-skill of nextflow-pipelines: Step 3: Run Test Profile.
Scanned 9/9/2026
Install to Claude Code
Skills Directorynpx -y skills add vamseeachanta/workspace-hub --skill step-3-run-test-profile --agent claude-codeInstalls into .claude/skills of the current project.
Are you the author of Step 3 Run Test Profile?
Add the live security badge to your README — it updates automatically with every re-scan.
[](https://www.skillsdirectory.com/skills/vamseeachanta-step-3-run-test-profile-workspace-hub)More formats (shields.io, HTML) on the badges page.
---
name: nextflow-pipelines-step-3-run-test-profile
description: 'Sub-skill of nextflow-pipelines: Step 3: Run Test Profile.'
version: 1.0.0
category: science
type: reference
scripts_exempt: true
---
# 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).
---
Is this your skill, or is something wrong with this listing? Request removal or report an issue. Author removals are honored within 72 hours.
No comments yet. Be the first to comment!
Build reusable Terraform modules for AWS, Azure, and GCP infrastructure following infrastructure-as-code best practices. Use when creating infrastructure modules, standardizing cloud provisioning, or implementing reusable IaC components.
Wire a service's OpenTelemetry output to Sematext Cloud. Walks through region, App-type, instrumentation flow (managed OTLP endpoint vs Sematext Agent), and signal selection (traces/metrics/logs), then produces the exact env-var block and points at a runnable reference example in this repo. Invoke when instrumenting a new app for Sematext.
Deployment workflows, CI/CD pipeline patterns, Docker containerization, health checks, rollback strategies, and production readiness checklists for web applications. Use when setting up deployment infrastructure or planning releases.
Watch a pull request or review cycle until it is ready to merge. Use when asked to babysit, monitor, or keep checking PR comments, reviews, and CI until all actionable issues are resolved.
Interact with the Paperclip control plane API for task coordination and governance. Use when checking assignments, updating issue status, posting comments, delegating work, managing routines, or calling Paperclip API endpoints.
