bio-nextflow-manager — independently scanned and version-tracked by SaferSkills.
SaferSkills independently audited bio-nextflow-manager (Agent Skill) and scored it 100/100 (green). The audit ran 55 deterministic rules across Security, Supply Chain, Maintenance, Transparency, and Community; it found 0 high-severity and 0 lower-severity findings. The full rule-by-rule trace and per-finding evidence are below. Free, methodology-open.
Findings & checks · 0 flagged
Every scanned point with the score it earned and what moved between them.
First recorded scan — no prior version to compare against.
The primary manifest — the file an agent reads to learn what this artifact does.
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.
- [ ] 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 outputsSkip 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.csvDECISION POINT: After fetching study info, confirm with user:
Then continue to Step 1.
Run first. Pipeline will fail without passing environment.
python src-tauri/resources/packs/bio-informatics-pack/nextflow-pipelines/scripts/check_environment.pyAll critical checks must pass. If any fail, provide fix instructions (Docker, Nextflow, Java).
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~30 seconds. Free. No account. Every finding cites a rule and a line of evidence.