# Nextflow Pipelines

> Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data for gene expression, variant calling, and chromatin accessibility analyses.

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

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# Nextflow Pipelines

## References

- [references/geo-sra-acquisition.md](references/geo-sra-acquisition.md) - Downloading public GEO/SRA data
- [references/troubleshooting.md](references/troubleshooting.md) - Common issues and fixes
- [references/installation.md](references/installation.md) - Environment setup
- [references/pipelines/rnaseq.md](references/pipelines/rnaseq.md) - RNA-seq pipeline details
- [references/pipelines/sarek.md](references/pipelines/sarek.md) - Variant calling details
- [references/pipelines/atacseq.md](references/pipelines/atacseq.md) - ATAC-seq details

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## Sub-Skills

- [Quick Reference](quick-reference/SKILL.md)

## Sub-Skills

- [Workflow Checklist](workflow-checklist/SKILL.md)
- [Step 0: Acquire Data (GEO/SRA Only)](step-0-acquire-data-geosra-only/SKILL.md)
- [Docker issues (+2)](docker-issues/SKILL.md)
- [Step 2: Select Pipeline](step-2-select-pipeline/SKILL.md)
- [Step 3: Run Test Profile](step-3-run-test-profile/SKILL.md)
- [Generate automatically (+2)](generate-automatically/SKILL.md)
- [5a. Check genome availability (+2)](5a-check-genome-availability/SKILL.md)
- [Check completion (+1)](check-completion/SKILL.md)
- [Disclaimer](disclaimer/SKILL.md)
- [Attribution](attribution/SKILL.md)
- [Licenses](licenses/SKILL.md)