Agent skill
nextflow-pipelines
Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data for gene expression, variant calling, and chromatin accessibility analyses.
Install this agent skill to your Project
npx add-skill https://github.com/vamseeachanta/workspace-hub/tree/main/.claude/skills/science/bio-research/nextflow-pipelines
SKILL.md
Nextflow Pipelines
References
- references/geo-sra-acquisition.md - Downloading public GEO/SRA data
- references/troubleshooting.md - Common issues and fixes
- references/installation.md - Environment setup
- references/pipelines/rnaseq.md - RNA-seq pipeline details
- references/pipelines/sarek.md - Variant calling details
- references/pipelines/atacseq.md - ATAC-seq details
Sub-Skills
- Quick Reference
Sub-Skills
- Workflow Checklist
- Step 0: Acquire Data (GEO/SRA Only)
- Docker issues (+2)
- Step 2: Select Pipeline
- Step 3: Run Test Profile
- Generate automatically (+2)
- 5a. Check genome availability (+2)
- Check completion (+1)
- Disclaimer
- Attribution
- Licenses
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