nextflow-development
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.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill nextflow-development --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# nf-core Pipeline Deployment 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. ## Workflow Checklist ``` - [ ] Step 0: Acquire data (if from GEO/SRA) - [ ] Step 1: Environment check (MUST pass) - [ ] Step 2: Select pipeline (confirm with user) - [ ] Step 3: Run test profile (MUST pass) - [ ] Step 4: Create samplesheet - [ ] Step 5: Configure & run (confirm genome with user) - [ ] Step 6: Verify outputs ``` --- ## 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 ``
- Workflow Checklist
- Step 0: Acquire Data (GEO/SRA Only)
- Step 1: Environment Check
- Docker issues
- Nextflow issues
- Java issues
- Step 2: Select Pipeline
- Step 3: Run Test Profile
- Step 4: Create Samplesheet
- Generate automatically
- Validate existing samplesheet
- Samplesheet formats
- Step 5: Configure & Run
- 5a. Check genome availability
python scripts/sra_geo_fetch.py info GSE110004 python scripts/sra_geo_fetch.py download GSE110004 -o ./fastq -i python scripts/sra_geo_fetch.py samplesheet GSE110004 --fastq-dir ./fastq -o samplesheet.csv python scripts/check_environment.py python scripts/detect_data_type.py /path/to/data nextflow run nf-core/<pipeline> -r <version> -profile test,docker --outdir test_output ls test_output/multiqc/multiqc_report.html grep "Pipeline completed successfully" .nextflow.log python scripts/generate_samplesheet.py /path/to/data <pipeline> -o samplesheet.csv python scripts/generate_samplesheet.py --validate samplesheet.csv <pipeline>
What does the nextflow-development skill do?
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.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill nextflow-development --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.