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 agentmods add instructions/friendsofstrandseq/mosaicatcher-pipeline/gemini-mdgit clone --depth 1 https://github.com/friendsofstrandseq/mosaicatcher-pipelineWrote 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/instructions/friendsofstrandseq/mosaicatcher-pipeline/gemini-md)<a href="https://agentmods.dev/instructions/friendsofstrandseq/mosaicatcher-pipeline/gemini-md"><img src="https://agentmods.dev/badge/instructions/friendsofstrandseq/mosaicatcher-pipeline/gemini-md.svg" alt="Measured on agentmods" 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 | $0.02434 | $0.02434 |
| Opus 5 | $0.01217 | $0.01217 |
| Sonnet 5 | $0.00487 | $0.00487 |
| Haiku 4.5 | $0.00243 | $0.00243 |
Grade A, and why
mosaicatcher-pipeline GEMINI.md scanned grade A with 0 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 3d 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.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
This is a copy
94% identical to mosaicatcher-pipeline CLAUDE.md — 57 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 — 232 lines — stays where its author put it; the contents beside it link to each section on GitHub.
CLAUDE.md
This file provides guidance to Gemini CLI (Gemini CLI) when working with code in this repository.
Project Overview
MosaiCatcher-pipeline is a Snakemake workflow for structural variant (SV) calling from single-cell Strand-seq sequencing data. The pipeline processes BAM files through binning, strand state detection, segmentation, haplotype resolution, and SV classification.
Current Version: 2.4.0-beta.2 Documentation: https://friendsofstrandseq.github.io/mosaicatcher-docs/
Version Management
The project uses a centralized version management system with support for stable and beta releases:
- Version file:
VERSION(single-line file at repo root) - Automated bumping:
- Stable:
pixi run bump-patch|bump-minor|bump-major - Beta:
pixi run bump-beta(increment beta),pixi run bump-release(toggle beta/stable)
- Stable:
- Config file:
.bumpversion.cfg(defines which files to update) - Container tags: Assembly-specific with version
- Stable:
ghcr.io/.../mosaicatcher-pipeline:hg38-2.3.5 - Beta:
ghcr.io/.../mosaicatcher-pipeline:hg38-2.3.6-beta.1
- Stable:
When you bump version:
VERSION,pixi.toml,config/config.yaml, andCLAUDE.mdare automatically updated- Git commit and tag are created automatically
- Push tag to trigger container build workflow
- Release creation automatically generates formatted changelog from commits
Beta releases support iterative testing before stable release. Changelog generator categorizes commits (feat/fix/refactor/docs/etc) and includes PR links.
See docs/version-management.md for detailed documentation.
Common Commands
Using Pixi (Recommended for Snakemake v9+)
The project now uses Pixi for package management. Pixi provides better dependency resolution and is configured in pixi.toml.
Dry-run (validate workflow) - MosaiCatcher:
~/.pixi/bin/pixi run snakemake --cores 1 \
--configfile .tests/config/simple_config_mosaicatcher.yaml \
--sdm conda --conda-frontend mamba --dry-run
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.
- 3d ago First seen · 232 lines · 2,434 tokens per session scan A 7bcc814d9764
mosaicatcher-pipeline GEMINI.md is an instructions file published in the GitHub repository friendsofstrandseq/mosaicatcher-pipeline (26 stars, last pushed 4d ago), licensed MIT. It adds 2,434 tokens to every session, about $0.0122 per session on Opus 5. A static security scan graded it A with 0 findings. It is 94% identical to mosaicatcher-pipeline CLAUDE.md, differing in 57 lines, and is treated as a copy.
Other instructions, from other repositories
autozyme CLAUDE.md
Instructions for ElliotXie/autozyme, covering autozyme, layout, how to use, environment and cli quick reference.
opentargets-mcp AGENTS.md
Instructions for nickzren/opentargets-mcp, covering agent guide — opentargets-mcp, what this server is, run locally (stdio), use this server for and triage hints.
open-genome-agent AGENTS.md
Instructions for 45ck/open-genome-agent, covering agents.md, core policy, mission, mandatory rules and delegation rules.
mygene-mcp AGENTS.md
AGENTS.md instructions for nickzren/mygene-mcp, covering agent guide — mygene-mcp, what this server is, run locally (stdio), use this server for and triage hints.
Heuris-BioMCP CLAUDE.md
Claude Code instructions for SachinGawande2003/Heuris-BioMCP, covering heuris-biomcp agent guidance, what this server is for, recommended workflows, literature and mechanism grounding and translational gene review.
gnomad-genetics-mcp-server AGENTS.md
AGENTS.md instructions for cyanheads/gnomad-genetics-mcp-server, covering developer protocol, core rules, patterns, server config (src/config/server-config.ts) and server identity and instructions.