github.com/MultiQC/MultiQC (link)

You are an expert programming assistant helping build a project called MultiQC.

Base MultiQC codebase is written in Python 3.9+. Code should use type hints, and it's checked with mypy.

Pydantic should be used to validate configs coming from user.

Plotly is used to build plots. Plotly Python library creates plot objects that a dumped to JSON, which is compressed and embedded into the portable HTML report, where it's loaded and rendered by frontend using Plotly-JS library.

The frontend is written with Jav

docs/images
docs/markdown/modules

# CLAUDE.md

Guidance for Claude Code (claude.ai/code) when working in this repository.

## IMPORTANT

Never push to main. When asked to add a change or open a PR, check the
current branch first; if it's `main`, create a new branch and push to that.

Do NOT create a `Pipfile` — this project uses `pyproject.toml`.

## Style and conventions

- Python 3.9+. Use f-strings and other modern Python 3 syntax. Do not use
  `__future__` imports or `OrderedDict`.
- Double quotes for strings.
- No shebang lines on Py

# CLAUDE.md - MultiQC Default Template

This file provides guidance for working with the MultiQC default template frontend assets.

## Overview

The default template is the main HTML report template for MultiQC. It uses Bootstrap 5.3.7 for styling and layout, with custom JavaScript for interactive features like plot rendering, sample filtering, and toolbox controls.

## Directory Structure

```
multiqc/templates/default/
├── assets/           # Third-party libraries (jQuery, Plotly.js, Bootstrap icons

name: Claude Code Review

on:
  # workflow_run is intentional: the trigger workflow runs in the unprivileged
  # PR context and only uploads an artifact; this workflow consumes it from
  # the privileged base-repo context. Removing it would either lose fork-PR
  # support or leak ANTHROPIC_API_KEY to fork contexts.
  workflow_run: # zizmor: ignore[dangerous-triggers]
    workflows: ["Claude Code Review Trigger"]
    types:
      - completed

jobs:
  claude-review:
    # Only run if the trigger workflow succ

name: Claude Code

on:
  issue_comment:
    types: [created]
  pull_request_review_comment:
    types: [created]
  issues:
    types: [opened, assigned]
  pull_request_review:
    types: [submitted]

jobs:
  claude:
    if: |
      (github.event_name == 'issue_comment' && contains(github.event.comment.body, '@claude')) ||
      (github.event_name == 'pull_request_review_comment' && contains(github.event.comment.body, '@claude')) ||
      (github.event_name == 'pull_request_review' && contains(github.event.r

---
name: triaging-module-requests
description: |
  Triage MultiQC `module: new` GitHub issues: calculate 0-100 priority scores, apply priority labels, post analysis comments with score breakdowns, and give contributors actionable feedback to improve their request. Use when a new `module: new` issue is opened, when a user comments `@claude analyze-module` on a request, during weekly bulk triage, or when manually re-evaluating a module request.
---

# Triage MultiQC Module Requests

Invoked by `.github/workf

---
name: reviewing-prs
description: |
  Review MultiQC pull requests or local branch diffs. Scan changes for anti-patterns against the project's rules, check PR hygiene (issue link, test data, screenshots), and produce a structured comment with severity-tagged findings. Use when the user asks to review a MultiQC PR, asks for feedback on a branch/diff, runs `gh pr view`/`gh pr diff`, or wants a code review of MultiQC changes (new modules, plot tweaks, core refactors, docs, anything).
---

# Review MultiQC P

---
name: implementing-new-modules
description: |
  Create a new MultiQC module from scratch. Parse a bioinformatics tool's output, register search patterns and entry points, add general stats columns, build plots and sections, write tests, open a PR. Use when implementing a `module: new` GitHub issue, when the user asks to add support for a new tool, or when adding a parser for a new tool output format.
---

# Implement New MultiQC Module

## Workflow

1. **Research the tool**: read its docs, get example o