Nextflow Pipelines

---
name: nextflow-pipelines
description: Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing
  data for gene expression, variant calling, and chromatin accessibility analyses.
type: reference
version: 1.0.0
category: science
last_updated: 2026-02-03
source: https://github.com/anthropics/knowledge-work-plugins
related_skills:
- single-cell-rna-qc
- scvi-tools
- clinical-trial-protocol
- instrument-data-allotrope
- scientific-problem-selection
capabilities: []
requires: []
tags: []
scripts_exempt: true
---

# 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

---

## 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)