What is mosaicatcher-pipeline GEMINI.md?

Repository-specific instructions for working on MosaiCatcher-pipeline, a Snakemake workflow that analyzes single-cell Strand-seq data to find structural DNA changes.

Use it when developing, running, or releasing the MosaiCatcher-pipeline, including work with Snakemake and pixi.

It gives an agent the project context, versioning rules, and recommended commands so changes follow the repository's established workflow.

How friendsofstrandseq/mosaicatcher-pipeline configures Gemini CLI

Reuse

Borrowing it

Nothing to install: this file belongs to friendsofstrandseq/mosaicatcher-pipeline. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file

curl -O https://raw.githubusercontent.com/friendsofstrandseq/mosaicatcher-pipeline/main/GEMINI.md

Clone the repo

git clone --depth 1 https://github.com/friendsofstrandseq/mosaicatcher-pipeline

Made for: Gemini CLI.

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/instructions/friendsofstrandseq/mosaicatcher-pipeline/gemini-md/github.svg)](https://agentmods.dev/instructions/friendsofstrandseq/mosaicatcher-pipeline/gemini-md)

Your own site

<a href="https://agentmods.dev/instructions/friendsofstrandseq/mosaicatcher-pipeline/gemini-md"><img src="https://agentmods.dev/badge/instructions/friendsofstrandseq/mosaicatcher-pipeline/gemini-md/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/instructions/friendsofstrandseq/mosaicatcher-pipeline/gemini-md"><img src="https://agentmods.dev/badge/instructions/friendsofstrandseq/mosaicatcher-pipeline/gemini-md.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 2,434 This file is loaded in full into every session.

When invoked 2,434 The same file — it is already loaded in full.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin 94% 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	$0.02434	$0.02434
Opus 5.5	$0.00974	$0.00974
Sonnet 5.5	$0.00487	$0.00487
Haiku 4.5	$0.00243	$0.00243

Measured 2mo ago against content hash 7bcc814d9764, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

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 2mo 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.

Origin

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.

GEMINI.md · 232 lines

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)
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

When you bump version:

VERSION, pixi.toml, config/config.yaml, and CLAUDE.md are 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

Read the full file on GitHub · 232 lines

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.

2mo ago First seen · 232 lines · 2,434 tokens per session scan A 7bcc814d9764

Subscribe to this mod's changes

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 $0.0097 per session on Opus 5.5. 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.

DevOps and cloud Scientific bioinformatics genomics mosaicatcher pipeline snakemake strand-seq

mosaicatcher-pipeline GEMINI.md next to 6 instructions from other repositories
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mosaicatcher-pipeline: Instructions file for Gemini CLI