# Nextflow Pipelines Step 0 Acquire Data Geosra Only

> Sub-skill of nextflow-pipelines: Step 0: Acquire Data (GEO/SRA Only).

- Skill: `vamseeachanta/nextflow-pipelines-step-0-acquire-data-geosra-only` (Agent Skill)
- Install (CLI): `npx skillmds@latest add vamseeachanta/nextflow-pipelines-step-0-acquire-data-geosra-only`
- Raw SKILL.md: https://api.skillmd.com/api/skills/vamseeachanta/nextflow-pipelines-step-0-acquire-data-geosra-only/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-step-0-acquire-data-geosra-only

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# Step 0: Acquire Data (GEO/SRA Only)

## Step 0: Acquire Data (GEO/SRA Only)


**Skip this step if user has local FASTQ files.**

For public datasets, fetch from GEO/SRA first. See [references/geo-sra-acquisition.md](references/geo-sra-acquisition.md) for the full workflow.

**Quick start:**

```bash
# 1. Get study info
python scripts/sra_geo_fetch.py info GSE110004

# 2. Download (interactive mode)
python scripts/sra_geo_fetch.py download GSE110004 -o ./fastq -i

# 3. Generate samplesheet
python scripts/sra_geo_fetch.py samplesheet GSE110004 --fastq-dir ./fastq -o samplesheet.csv
```

**DECISION POINT:** After fetching study info, confirm with user:
- Which sample subset to download (if multiple data types)
- Suggested genome and pipeline

Then continue to Step 1.

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