Agent skill
nextflow-pipelines-step-0-acquire-data-geosra-only
Sub-skill of nextflow-pipelines: Step 0: Acquire Data (GEO/SRA Only).
Install this agent skill to your Project
npx add-skill https://github.com/vamseeachanta/workspace-hub/tree/main/.claude/skills/_archive/science/bio-research/nextflow-pipelines/step-0-acquire-data-geosra-only
SKILL.md
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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