# Nextflow Pipelines 5a Check Genome Availability

> Sub-skill of nextflow-pipelines: 5a. Check genome availability (+2).

- Skill: `vamseeachanta/nextflow-pipelines-5a-check-genome-availability` (Agent Skill)
- Install (CLI): `npx skillmds@latest add vamseeachanta/nextflow-pipelines-5a-check-genome-availability`
- Raw SKILL.md: https://api.skillmd.com/api/skills/vamseeachanta/nextflow-pipelines-5a-check-genome-availability/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-5a-check-genome-availability

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# 5a. Check genome availability (+2)

## 5a. Check genome availability


```bash
python scripts/manage_genomes.py check <genome>
# If not installed:
python scripts/manage_genomes.py download <genome>
```

Common genomes: GRCh38 (human), GRCh37 (legacy), GRCm39 (mouse), R64-1-1 (yeast), BDGP6 (fly)

## 5b. Decision points


**DECISION POINT: Confirm with user:**

1. **Genome:** Which reference to use
2. **Pipeline-specific options:**
   - **rnaseq:** aligner (star_salmon recommended, hisat2 for low memory)
   - **sarek:** tools (haplotypecaller for germline, mutect2 for somatic)
   - **atacseq:** read_length (50, 75, 100, or 150)

## 5c. Run pipeline


```bash
nextflow run nf-core/<pipeline> \
    -r <version> \
    -profile docker \
    --input samplesheet.csv \
    --outdir results \
    --genome <genome> \
    -resume
```


*See sub-skills for full details.*