Data & ReproBioinformatics & GenomicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

nextflow-development

Maintainer FreedomIntelligence · Last updated April 1, 2026

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.

OpenClawNanoClawAnalysisReproductionnextflow-development🧬 bioinformatics (gptomics bio-* suite)bioinformatics tools & pipelinesrun

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/nextflow-development

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

Run nf-core bioinformatics pipelines on local or public sequencing data.
Target users: Bench scientists and researchers without specialized bioinformatics training who need to run large-scale omics analyses—differential expression, variant calling, or chromatin accessibility analysis.
python scripts/sra_geo_fetch.py info GSE110004.

Source Doc

Excerpt From SKILL.md

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: