bio-nextflow-manager

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:

# Set path to pack scripts
$PACK_SCRIPTS = "src-tauri/resources/packs/bio-informatics-pack/nextflow-pipelines/scripts"

# 1. Get study info
python $PACK_SCRIPTS/sra_geo_fetch.py info GSE110004

# 2. Download (interactive mode)
python $PACK_SCRIPTS/sra_geo_fetch.py download GSE110004 -o ./fastq -i

# 3. Generate samplesheet
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