| name | bio-nextflow-manager |
| description | 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. |
| requires | ["python","bash"] |
nf-core Pipeline Deployment
Run nf-core bioinformatics pipelines on local or public sequencing data.
Note: This skill utilizes the Bio-Informatics Pack.
Scripts and references are located in: src-tauri/resources/packs/bio-informatics-pack/nextflow-pipelines/
Target users: Bench scientists and researchers without specialized bioinformatics training who need to run large-scale omics analyses.
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 pack's references/geo-sra-acquisition.md.
Quick start:
$PACK_SCRIPTS = "src-tauri/resources/packs/bio-informatics-pack/nextflow-pipelines/scripts"
python $PACK_SCRIPTS/sra_geo_fetch.py info GSE110004
python $PACK_SCRIPTS/sra_geo_fetch.py download GSE110004 -o ./fastq -i
python $PACK_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.
Step 1: Environment Check
Run first. Pipeline will fail without passing environment.
python src-tauri/resources/packs/bio-informatics-pack/nextflow-pipelines/scripts/check_environment.py
All critical checks must pass. If any fail, provide fix instructions (Docker, Nextflow, Java).
Step 2: Select Pipeline
DECISION POINT: Confirm with user before proceeding.
| Data Type | Pipeline | Goal |
|---|
| RNA-seq | rnaseq | Gene expression |
| WGS/WES | sarek | Variant calling |
| ATAC-seq | atacseq | Chromatin accessibility |
Auto-detect from data:
python src-tauri/resources/packs/bio-informatics-pack/nextflow-pipelines/scripts/detect_data_type.py /path/to/data
