Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add sun2443/designer-skills --skill nextflow-developmentgit clone --depth 1 https://github.com/sun2443/designer-skillsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/sun2443/designer-skills/nextflow-development)<a href="https://agentmods.dev/skills/sun2443/designer-skills/nextflow-development"><img src="https://agentmods.dev/badge/skills/sun2443/designer-skills/nextflow-development/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/sun2443/designer-skills/nextflow-development"><img src="https://agentmods.dev/badge/skills/sun2443/designer-skills/nextflow-development.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00095 | $0.02354 |
| Opus 5.5 | $0.00038 | $0.00942 |
| Sonnet 5.5 | $0.00019 | $0.00471 |
| Haiku 4.5 | $0.00010 | $0.00235 |
Grade D, and why
nextflow-development scanned grade D with 3 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 13d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Asks for rootmediumPrivilege escalation
A mod that escalates privileges can change anything on the machine, not only the project.
| Permission denied | `sudo usermod -aG docker $USER` then re-login | Downloads and executes remote codehighSupply chain
curl | sh runs whatever the server returns today, which is not necessarily what it returned when this was reviewed.
| Not installed | `curl -s https://get.nextflow.io \| bash && mv nextflow ~/bin/` | Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
| Not installed | `curl -s https://get.nextflow.io \| bash && mv nextflow ~/bin/` | This is a copy
100% identical to nextflow-development — 0 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 291 lines — stays where its author put it; the contents beside it link to each section on GitHub.
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 for the full workflow.
Quick start:
# 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
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 scripts/check_environment.py
All critical checks must pass. If any fail, provide fix instructions:
Docker issues
| Problem | Fix |
|---|---|
| Not installed | Install from https://docs.docker.com/get-docker/ |
| Permission denied | sudo usermod -aG docker $USER then re-login |
| Daemon not running | sudo systemctl start docker |
Nextflow issues
| Problem | Fix |
|---|---|
| Not installed | curl -s https://get.nextflow.io | bash && mv nextflow ~/bin/ |
| Version < 23.04 | nextflow self-update |
What ships with it
21 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
- LICENSE.txt 10 KB
- references/geo-sra-acquisition.md 14 KB
- references/installation.md 1.8 KB
- references/pipelines/atacseq.md 4.1 KB
- references/pipelines/rnaseq.md 3.5 KB
- references/pipelines/sarek.md 3.9 KB
- references/troubleshooting.md 3.3 KB
- scripts/check_environment.py 14 KB runs code
- scripts/config/genomes.yaml 3.4 KB
- scripts/config/pipelines/atacseq.yaml 5.0 KB
- scripts/config/pipelines/rnaseq.yaml 4.1 KB
- scripts/config/pipelines/sarek.yaml 6.1 KB
- scripts/detect_data_type.py 9.7 KB runs code
- scripts/generate_samplesheet.py 15 KB runs code
- scripts/manage_genomes.py 16 KB runs code
- scripts/sra_geo_fetch.py 24 KB runs code
- scripts/utils/__init__.py 1.7 KB runs code
- scripts/utils/file_discovery.py 5.0 KB runs code
- scripts/utils/ncbi_utils.py 28 KB runs code
- scripts/utils/sample_inference.py 7.7 KB runs code
- scripts/utils/validators.py 8.2 KB runs code
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 13d ago First seen · 291 lines · 95 tokens per session scan D f30017df5d49
nextflow-development is a skill published in the GitHub repository sun2443/designer-skills (0 stars, last pushed 6mo ago), licensed Apache-2.0. It adds 95 tokens to every session and 2,354 once invoked, about $0.0004 per session on Opus 5.5. A static security scan graded it D with 3 findings (asks for root, downloads and executes remote code, makes network calls). It is 100% identical to nextflow-development, differing in 0 lines, and is treated as a copy.
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