nextflow-pipelines-step-0-acquire-data-geosra-only

name	nextflow-pipelines-step-0-acquire-data-geosra-only
description	Sub-skill of nextflow-pipelines: Step 0: Acquire Data (GEO/SRA Only).
version	1.0.0
category	science
type	reference
scripts_exempt	true

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 for the full workflow.

Quick start:

# 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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