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数据与复现
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nextflow-development
维护者 FreedomIntelligence · 最近更新 2026年4月1日
Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core, Nextflow, FASTQ analysis, variant calling, gene expression, differential expression, GEO reanalysis, GSE/GSM/SRR accessions, or samplesheet creation.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/nextflow-development
- 维护者
- FreedomIntelligence
- 许可
- MIT
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- 运行 nf-core bioinformatics pipelines on local 或 public sequencing data。
- Target users：Bench scientists 、 researchers without specialized bioinformatics training who need to run large-scale omics analyses—differential expression，variant calling，或 chromatin accessibility analysis。
- python scripts/sra_geo_fetch.py info GSE110004。
原始文档
SKILL.md 摘录
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:
## 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.
适用场景
- 适合在analyzing RNA-seq，WGS/WES，或 ATAC-seq data—either local FASTQs 或 public 数据集s ，面向 GEO/SRA时使用。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
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