What is nextflow-development?

A workflow for running nf-core bioinformatics pipelines with Nextflow, a tool for executing repeatable data-analysis steps. It handles sequencing data such as FASTQ files from local experiments or public repositories like GEO and SRA.

Use it for RNA sequencing gene-expression analysis, whole-genome or exome variant calling, and ATAC-seq chromatin-accessibility analysis.

It guides researchers through choosing a pipeline, preparing samples, checking the setup, running the analysis, and verifying results without requiring specialist bioinformatics training.

nextflow-development — Skill for Claude Code and Codex by Shoko-offici

Install

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.

Any agent

npx skills add Shoko-official/Claude-Science-System-Prompts --skill nextflow-development

Clone the repo

git clone --depth 1 https://github.com/Shoko-official/Claude-Science-System-Prompts

Made for: Claude Code, Codex.

Wrote 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.

README.md

[![agentmods](https://agentmods.dev/badge/skills/shoko-official/claude-science-system-prompts/nextflow-development/github.svg)](https://agentmods.dev/skills/shoko-official/claude-science-system-prompts/nextflow-development)

Your own site

<a href="https://agentmods.dev/skills/shoko-official/claude-science-system-prompts/nextflow-development"><img src="https://agentmods.dev/badge/skills/shoko-official/claude-science-system-prompts/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.

Your own site · 80×15

<a href="https://agentmods.dev/skills/shoko-official/claude-science-system-prompts/nextflow-development"><img src="https://agentmods.dev/badge/skills/shoko-official/claude-science-system-prompts/nextflow-development.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 95 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 2,354 The whole file, excluding the scripts and references it only reads on demand.

Security scan D 3 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin 100% copy Near-identical to another mod in the catalogue.

Token cost

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	$0.00048	$0.01177
Sonnet 5	$0.00019	$0.00471
Haiku 4.5	$0.00010	$0.00235

Measured 12d ago against content hash f30017df5d49, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-11, from the pricing page.

Security

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 12d ago.

The scan reads SKILL.md. This mod also ships 10 executable files (scripts/check_environment.py, scripts/detect_data_type.py, scripts/generate_samplesheet.py, …), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

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/` |

Origin

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.

skills/nextflow-development/SKILL.md · 291 lines

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`

Read the full file on GitHub · 291 lines

Files

What ships with it

20 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.

Changes

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.

12d ago First seen · 291 lines · 95 tokens per session scan D f30017df5d49

Subscribe to this mod's changes

nextflow-development is a skill published in the GitHub repository Shoko-official/Claude-Science-System-Prompts (10 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 95 tokens to every session and 2,354 once invoked, about $0.0005 per session on Opus 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.

Scientific agentic-ai ai-agents anthropic claude claude-science-ai fable

nextflow-development