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Execute ENCODE ATAC-seq processing pipeline from FASTQ to peaks and signal tracks. Child of pipeline-guide. Provides stage-by-stage Nextflow execution with Docker containers and cloud deployment. Handles Tn5 transposase offset correction, mitochondrial read removal, and nucleosome-free fragment selection. Use when users need to process ATAC-seq data following ENCODE standards. Trigger on: ATAC-seq pipeline, run ATAC-seq, process ATAC-seq, chromatin accessibility, open chromatin, Tn5 shift, TSS enrichment.

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Execute CUT&RUN processing pipeline from FASTQ to peaks and signal tracks. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing CUT&RUN or CUT&Tag data, an alternative to ChIP-seq with lower background. Trigger on: CUT&RUN pipeline, CUT&Tag, SEACR, Henikoff, targeted chromatin, pA-MNase, process CUT&RUN.

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Execute ENCODE RNA-seq pipeline from FASTQ to gene quantification and signal tracks. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing RNA-seq data with STAR alignment, RSEM/Kallisto quantification, or generating expression matrices. Trigger on: RNA-seq pipeline, gene expression, STAR alignment, RSEM quantification, transcript quantification, TPM, FPKM, RNA processing, run RNA-seq.

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Execute ENCODE Hi-C pipeline from FASTQ to contact matrices and loop calls. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing Hi-C data, generating contact matrices, or calling loops. Trigger on: Hi-C pipeline, chromatin conformation, contact matrix, loop calling, TAD detection, Juicer, HiCCUPS, 3D genome.

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Generate publication-ready methods sections, figure legends, supplementary tables, and data availability statements from ENCODE analysis provenance. Implements the scientific documentation standards requiring complete metadata reporting. Use when the user needs to write methods, generate figure legends, create supplementary tables, draft data availability statements, compile tool citations, or auto-generate any publication text from their ENCODE analysis. Trigger on: methods section, figure legend, supplementary table, data availability, tool citations, publication writing, manuscript, write methods, methods draft, write up, write-up, paper writing, reproducible methods.

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Execute ENCODE ChIP-seq processing pipeline from FASTQ to peaks and signal tracks. Child of pipeline-guide. Provides stage-by-stage Nextflow execution with Docker containers and cloud deployment. Use when users need to process ChIP-seq data following ENCODE standards, run peak calling with MACS2, perform IDR analysis, or generate signal tracks. Trigger on: ChIP-seq pipeline, run ChIP-seq, process ChIP-seq, MACS2 peak calling, IDR analysis, ChIP-seq FASTQ processing.

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Creates Mermaid and ASCII diagrams for flowcharts, architecture, ERDs, state machines, mindmaps, and more. Use when user mentions diagram, flowchart, mermaid, ASCII diagram, text diagram, terminal diagram, visualize, C4, mindmap, architecture diagram, sequence diagram, ERD, or needs visual documentation.

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Scaffold or migrate a repository onto release-please. Generates release-please-config.json, .release-please-manifest.json, and a release-please.yml workflow, plus an opt-in menu of tag-keyed deploy/publish templates (Docker/ECR matrix, frontend host deploy, npm OIDC publish, GitHub Release asset, Fly.io deploy, generic). Supports monorepo (mutual exclude-paths matrix), single-package, and mixed-language (node/simple/python) repos. Use when user runs /release-please-setup, mentions "release please", "set up release please", "automate releases", "conventional-commit releases", "monorepo release automation", or "migrate to release-please".

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Analyzes git commit history and generates professional changelogs with semantic versioning, conventional commit support, and multiple output formats (Keep a Changelog, Conventional, GitHub). Use when editing CHANGELOG.md, CHANGELOG.txt, or HISTORY.md files, preparing release notes, creating releases, bumping versions, updating changelog, documenting changes, writing release notes, tracking changes, version bump, tag release, or when user mentions "changelog", "release notes", "version history", "release", "semantic versioning", or "conventional commits".

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Create Product Requirements Document (PRD) and setup for Ralph autonomous loop. Use when user runs /create-prd command, wants to set up a project for Ralph, mentions "ralph setup", "create prd", "product requirements", or needs to generate tasks for autonomous development.

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Install Taskfile (task) and scaffold or audit Taskfile.yml configurations with ecosystem-aware templates. Auto-detects Node.js/pnpm, JVM/Gradle, Python/uv, Docker, and recommends single-file or multi-file (includes) patterns based on project complexity. Use when user runs /devtools:taskfile-setup, mentions "taskfile setup", "setup task runner", "audit taskfile", "scaffold taskfile", "add taskfile", "taskfile.yml", or "developer tasks".

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Validate plugin content quality before release. Run skill-validator across plugins, verify marketplace.json completeness, check plugin.json version consistency, and detect broken documentation cross-references. Use when preparing a release, before running release.sh, or when user mentions "release check", "pre-release", "plugin-release-checker", or "release validation".

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Run a Lighthouse audit against any URL via the local Lighthouse CLI or the PageSpeed Insights API fallback, parse category scores and failed audits, and map every failed audit ID to its official Chrome docs page plus a one-line fix. Use when user says "lighthouse", "lighthouse audit", "run lighthouse", "lighthouse score", or "pagespeed".

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Pre-publish (or retroactive) content-quality gate implementing Google's official self-assessment questions from the creating-helpful-content doc, plus 2024 spam-policy red flags. Verdict: PUBLISH / REVISE / RETHINK. Use when user says "helpful content", "people-first", "content self-assessment", "is my content helpful", or "content quality gate".

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Standalone E-E-A-T scoring rubric for a URL or content draft. Scores Experience, Expertise, Authoritativeness, and Trust 0-5 each using concrete detectable signals, framed per Google's creating-helpful-content doc. Use when user says "E-E-A-T", "EEAT", "experience expertise", "trust signals", or "author authority".

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Audit a site or page against Google's OFFICIAL AI optimization guidance — readiness for AI Overviews and AI Mode, grounded in Google's published ai-optimization-guide and ai-features docs (not third-party GEO theory). Use when user says "AI optimization", "AI Overviews", "AI mode", "AI search readiness", "optimize for AI", or "GEO audit".

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Use this skill any time a spreadsheet file is the primary input or output. This means any task where the user wants to: open, read, edit, or fix an existing .xlsx, .xlsm, .csv, or .tsv file (e.g., adding columns, computing formulas, formatting, charting, cleaning messy data); create a new spreadsheet from scratch or from other data sources; or convert between tabular file formats. Trigger especially when the user references a spreadsheet file by name or path — even casually (like "the xlsx in my downloads") — and wants something done to it or produced from it. Also trigger for cleaning or restructuring messy tabular data files (malformed rows, misplaced headers, junk data) into proper spreadsheets. The deliverable must be a spreadsheet file. Do NOT trigger when the primary deliverable is a Word document, HTML report, standalone Python script, database pipeline, or Google Sheets API integration, even if tabular data is involved.

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Generate comprehensive OpenSpec specifications directly from the current project state. Use when the user wants to create or populate main specs by analyzing existing code, documentation, AGENTS.md, GitHub issues, and pull requests — without going through the change/proposal workflow. Ideal for bootstrapping specs on a project that already has working code but no specs yet, or for refreshing specs to match the current implementation.

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Create a new Azure DevOps wiki page. Use when the user wants to add a new wiki page, write project documentation in Azure DevOps wiki format, or update wiki page structure with mermaid diagrams in Traditional Chinese.

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Convert simplified Chinese to Traditional Chinese (zh-TW), covering characters, Taiwan vocabulary, and phrasing. Use when the user asks to convert 簡體 to 正體/繁體, localise mainland Chinese text for Taiwan, fix simplified characters left in a document or repository, check whether content is written in proper zh-TW, or normalise variant forms such as 着/裏/爲 to the Taiwan standard. Handles both files edited in place and text pasted into the conversation. Runs on Python 3 standard library alone, with no OpenCC and no installed packages.

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Add SLSA build-provenance attestations to existing GitHub Actions workflows. Use when the user wants to add artifact attestations, build provenance, or SLSA attestations to Docker container image builds in GitHub Actions CI/CD pipelines.

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Convert current conversation context into a structured Product Requirements Document (PRD) and optionally post it to GitHub Issues. Use before /supergraph:plan when requirements came from a conversation, user story, or feature discussion rather than a formal spec.

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Create a Software Design Document (SDD) defining component architecture, data contracts, API schemas, and platform compatibility before planning. Use in Tier 3 (Full Pipeline) or when modifying interfaces, hooks, databases, or multi-platform contracts.

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Compact current session context into a handoff document for seamless continuation in a new session. Use when context window is exhausted, switching machines, handing work to another agent, or ending a long session mid-task.

日本語の概要は準備中です。原文の説明を表示しています。