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Once the sample model is clear, hand off to the narrow subtype skill.\n\n## Essential Inputs\n\nConfirm:\n\n- data type: WGS, WES, or panel\n- sample model: germline single sample, cohort, trio, tumor-only, or tumor-normal\n- input type: FASTQ, BAM, or CRAM\n- organism and reference genome\n- known-sites resources for BQSR, if required\n- target BED for WES or panels\n- UMI or duplex handling\n- desired callers and annotation outputs\n\n## Dispatch\n\nRoute by biological\u002Fsample model:\n\n- Germline singleton, cohort, family, trio, WGS, WES, or ordinary inherited panel: `ngs-dna-germline-variants`\n- Tumor-normal, tumor-only, relapse-baseline, or other cancer somatic calling: `ngs-dna-somatic-variants`\n- UMI, duplex, molecular-barcode, or low-frequency targeted panel calling: `ngs-dna-umi-panel-variants`\n\nIf the request is ambiguous, ask only for the missing sample model and assay design needed to choose among these three. Do not run one generic variant workflow when the request needs subtype-specific assumptions.\n\n## Public Default\n\nPrefer `nf-core\u002Fsarek` for an end-to-end public workflow. Use direct GATK4, DeepVariant, samtools, or bcftools commands only for smaller, focused tasks or when the user explicitly wants a custom pipeline.\n\n## Preflight\n\n```bash\npython plugins\u002Fngs-analysis\u002Fscripts\u002Fngs_preflight.py --pipeline dna_variant_calling --emit-install-plan\n```\n\n## Local Execution Package\n\nFor a compact BAM\u002FCRAM-to-VCF run with a matching reference FASTA, use the plugin-owned samtools\u002Fbcftools runner:\n\n```bash\npython plugins\u002Fngs-analysis\u002Fscripts\u002Frun_dna_variant_calling.py \\\n  --sample-sheet dna_samples.tsv \\\n  --reference-fasta reference.fa \\\n  --region chr20:1-100000 \\\n  --filter-min-qual 30 \\\n  --filter-min-site-dp 10 \\\n  --execute\n```\n\nThe sample sheet should include `sample` and `bam` or `cram` columns. When `--region` is provided the runner also emits per-base depth plus a callable-loci summary for that interval, and when filter thresholds are provided it emits a soft-filtered VCF alongside the raw calls. This package is suitable for focused local checks and run-envelope generation; subtype skills still own germline, somatic, UMI, reference-resource, cohort, annotation, and workflow assumptions.\n\nThis compact runner now writes advisory `resources\u002Fresource_plan.json`, `resource_manifest.tsv`, `resource_env.sh`, and `resource_readiness.md` artifacts for the selected genome bundle. Use `--require-resource-plan` when missing registered reference resources should block readiness; otherwise the explicit `--reference-fasta` remains enough for focused local checks.\n\n## Kickoff Pattern\n\nPreflight-first nf-core pattern:\n\n```bash\nnextflow run nf-core\u002Fsarek \\\n  -profile test,docker \\\n  --outdir results\u002Fsarek_test\n```\n\nReal run skeleton:\n\n```bash\nnextflow run nf-core\u002Fsarek \\\n  -profile docker \\\n  --input samplesheet.csv \\\n  --outdir results\u002Fsarek \\\n  --genome GRCh38 \\\n  --tools haplotypecaller,vep\n```\n\nFor WES\u002Fpanel data, include the target BED. For tumor-normal data, verify pair metadata before execution. 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For tumor-normal data, verify pair metadata before execution. For UMI panels, preserve barcode handling and molecule-level QC.",{"type":39,"tag":54,"props":643,"children":645},{"id":644},"guardrails",[646],{"type":45,"value":647},"Guardrails",{"type":39,"tag":66,"props":649,"children":650},{},[651,656,661],{"type":39,"tag":70,"props":652,"children":653},{},[654],{"type":45,"value":655},"Do not mix genome builds across FASTA, GTF\u002FBED, known sites, and VEP cache.",{"type":39,"tag":70,"props":657,"children":658},{},[659],{"type":45,"value":660},"Do not download large references without confirming disk space and target path.",{"type":39,"tag":70,"props":662,"children":663},{},[664],{"type":45,"value":665},"Treat clinical interpretation as out of scope unless the user has a validated clinical workflow.",{"type":39,"tag":667,"props":668,"children":669},"style",{},[670],{"type":45,"value":671},"html .light .shiki span {color: var(--shiki-light);background: var(--shiki-light-bg);font-style: var(--shiki-light-font-style);font-weight: var(--shiki-light-font-weight);text-decoration: var(--shiki-light-text-decoration);}html.light .shiki span {color: var(--shiki-light);background: var(--shiki-light-bg);font-style: var(--shiki-light-font-style);font-weight: var(--shiki-light-font-weight);text-decoration: var(--shiki-light-text-decoration);}html .default .shiki span {color: var(--shiki-default);background: var(--shiki-default-bg);font-style: var(--shiki-default-font-style);font-weight: var(--shiki-default-font-weight);text-decoration: var(--shiki-default-text-decoration);}html .shiki span {color: var(--shiki-default);background: var(--shiki-default-bg);font-style: var(--shiki-default-font-style);font-weight: var(--shiki-default-font-weight);text-decoration: var(--shiki-default-text-decoration);}html .dark .shiki span {color: var(--shiki-dark);background: var(--shiki-dark-bg);font-style: var(--shiki-dark-font-style);font-weight: var(--shiki-dark-font-weight);text-decoration: var(--shiki-dark-text-decoration);}html.dark .shiki span {color: var(--shiki-dark);background: var(--shiki-dark-bg);font-style: var(--shiki-dark-font-style);font-weight: var(--shiki-dark-font-weight);text-decoration: var(--shiki-dark-text-decoration);}",{"items":673,"total":878},[674,695,718,735,751,770,789,805,821,835,847,862],{"slug":675,"name":675,"fn":676,"description":677,"org":678,"tags":679,"stars":692,"repoUrl":693,"updatedAt":694},"prior-auth-packet-builder","build healthcare prior authorization packets","Build a concise prior authorization packet from local case files and payer policy docs.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[680,683,686,689],{"name":681,"slug":682,"type":15},"Documents","documents",{"name":684,"slug":685,"type":15},"Healthcare","healthcare",{"name":687,"slug":688,"type":15},"Insurance","insurance",{"name":690,"slug":691,"type":15},"Regulatory Compliance","regulatory-compliance",28169,"https:\u002F\u002Fgithub.com\u002Fopenai\u002Fopenai-agents-python","2026-04-16T05:11:39.180399",{"slug":696,"name":696,"fn":697,"description":698,"org":699,"tags":700,"stars":715,"repoUrl":716,"updatedAt":717},"aspnet-core","build ASP.NET Core web applications","Build, review, refactor, or architect ASP.NET Core web applications using current official guidance for .NET web development. Use when working on Blazor Web Apps, Razor Pages, MVC, Minimal APIs, controller-based Web APIs, SignalR, gRPC, middleware, dependency injection, configuration, authentication, authorization, testing, performance, deployment, or ASP.NET Core upgrades.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[701,704,706,709,712],{"name":702,"slug":703,"type":15},".NET","dotnet",{"name":705,"slug":696,"type":15},"ASP.NET Core",{"name":707,"slug":708,"type":15},"Blazor","blazor",{"name":710,"slug":711,"type":15},"C#","csharp",{"name":713,"slug":714,"type":15},"Web Development","web-development",23787,"https:\u002F\u002Fgithub.com\u002Fopenai\u002Fskills","2026-04-12T05:07:02.819491",{"slug":719,"name":719,"fn":720,"description":721,"org":722,"tags":723,"stars":715,"repoUrl":716,"updatedAt":734},"chatgpt-apps","build ChatGPT Apps SDK applications","Build, scaffold, refactor, and troubleshoot ChatGPT Apps SDK applications that combine an MCP server and widget UI. Use when Codex needs to design tools, register UI resources, wire the MCP Apps bridge or ChatGPT compatibility APIs, apply Apps SDK metadata or CSP or domain settings, or produce a docs-aligned project scaffold. Prefer a docs-first workflow by invoking the openai-docs skill or OpenAI developer docs MCP tools before generating code.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[724,727,730,733],{"name":725,"slug":726,"type":15},"Apps SDK","apps-sdk",{"name":728,"slug":729,"type":15},"ChatGPT","chatgpt",{"name":731,"slug":732,"type":15},"MCP","mcp",{"name":9,"slug":8,"type":15},"2026-04-12T05:07:05.468097",{"slug":736,"name":736,"fn":737,"description":738,"org":739,"tags":740,"stars":715,"repoUrl":716,"updatedAt":750},"cli-creator","build CLIs from API docs","Build a composable CLI for Codex from API docs, an OpenAPI spec, existing curl examples, an SDK, a web app, an admin tool, or a local script. Use when the user wants Codex to create a command-line tool that can run from any repo, expose composable read\u002Fwrite commands, return stable JSON, manage auth, and pair with a companion skill.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[741,744,747],{"name":742,"slug":743,"type":15},"API Development","api-development",{"name":745,"slug":746,"type":15},"CLI","cli",{"name":748,"slug":749,"type":15},"Codex","codex","2026-04-12T05:07:04.132762",{"slug":752,"name":752,"fn":753,"description":754,"org":755,"tags":756,"stars":715,"repoUrl":716,"updatedAt":769},"cloudflare-deploy","deploy projects to Cloudflare","Deploy applications and infrastructure to Cloudflare using Workers, Pages, and related platform services. Use when the user asks to deploy, host, publish, or set up a project on Cloudflare.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[757,760,763,766],{"name":758,"slug":759,"type":15},"Cloudflare","cloudflare",{"name":761,"slug":762,"type":15},"Cloudflare Pages","cloudflare-pages",{"name":764,"slug":765,"type":15},"Cloudflare Workers","cloudflare-workers",{"name":767,"slug":768,"type":15},"Deployment","deployment","2026-04-12T05:07:14.275118",{"slug":771,"name":771,"fn":772,"description":773,"org":774,"tags":775,"stars":715,"repoUrl":716,"updatedAt":788},"define-goal","define and set measurable project goals","Help the user define a concrete, measurable goal before starting work, especially when they ask to use the goal tool, create a goal, set an objective, clarify success criteria, or turn a fuzzy intention into a quantitative outcome. Use this skill for goal creation and goal refinement only; it does not manage durable snapshots, decision logs, or long-running execution artifacts.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[776,779,782,785],{"name":777,"slug":778,"type":15},"Productivity","productivity",{"name":780,"slug":781,"type":15},"Project Management","project-management",{"name":783,"slug":784,"type":15},"Strategy","strategy",{"name":786,"slug":787,"type":15},"Task Management","task-management","2026-05-23T06:17:16.870838",{"slug":790,"name":790,"fn":791,"description":792,"org":793,"tags":794,"stars":715,"repoUrl":716,"updatedAt":804},"figma","translate Figma designs into code","Use the Figma MCP server to fetch design context, screenshots, variables, and assets from Figma, and to translate Figma nodes into production code. Trigger when a task involves Figma URLs, node IDs, design-to-code implementation, or Figma MCP setup and troubleshooting.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[795,798,800,803],{"name":796,"slug":797,"type":15},"Design","design",{"name":799,"slug":790,"type":15},"Figma",{"name":801,"slug":802,"type":15},"Frontend","frontend",{"name":731,"slug":732,"type":15},"2026-04-12T05:06:47.939943",{"slug":806,"name":806,"fn":807,"description":808,"org":809,"tags":810,"stars":715,"repoUrl":716,"updatedAt":820},"figma-code-connect-components","connect Figma designs to code components","Connects Figma design components to code components using Code Connect mapping tools. Use when user says \"code connect\", \"connect this component to code\", \"map this component\", \"link component to code\", \"create code connect mapping\", or wants to establish mappings between Figma designs and code implementations. For canvas writes via `use_figma`, use `figma-use`.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[811,812,815,816,817],{"name":796,"slug":797,"type":15},{"name":813,"slug":814,"type":15},"Design System","design-system",{"name":799,"slug":790,"type":15},{"name":801,"slug":802,"type":15},{"name":818,"slug":819,"type":15},"UI Components","ui-components","2026-05-10T05:59:52.971881",{"slug":822,"name":822,"fn":823,"description":824,"org":825,"tags":826,"stars":715,"repoUrl":716,"updatedAt":834},"figma-create-design-system-rules","generate design system rules from Figma","Generates custom design system rules for the user's codebase. Use when user says \"create design system rules\", \"generate rules for my project\", \"set up design rules\", \"customize design system guidelines\", or wants to establish project-specific conventions for Figma-to-code workflows. Requires Figma MCP server connection.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[827,828,829,832,833],{"name":796,"slug":797,"type":15},{"name":813,"slug":814,"type":15},{"name":830,"slug":831,"type":15},"Documentation","documentation",{"name":799,"slug":790,"type":15},{"name":801,"slug":802,"type":15},"2026-05-16T06:07:47.821474",{"slug":836,"name":836,"fn":837,"description":838,"org":839,"tags":840,"stars":715,"repoUrl":716,"updatedAt":846},"figma-implement-design","translate Figma designs into application code","Translates Figma designs into production-ready application code with 1:1 visual fidelity. Use when implementing UI code from Figma files, when user mentions \"implement design\", \"generate code\", \"implement component\", provides Figma URLs, or asks to build components matching Figma specs. For Figma canvas writes via `use_figma`, use `figma-use`.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[841,842,843,844,845],{"name":796,"slug":797,"type":15},{"name":799,"slug":790,"type":15},{"name":801,"slug":802,"type":15},{"name":818,"slug":819,"type":15},{"name":713,"slug":714,"type":15},"2026-05-16T06:07:40.583615",{"slug":848,"name":848,"fn":849,"description":850,"org":851,"tags":852,"stars":715,"repoUrl":716,"updatedAt":861},"hatch-pet","create animated pets for Codex","Create, repair, validate, visually QA, and package Codex-compatible animated pets and pet spritesheets from character art, generated images, company or prospect brand cues, or visual references. Use when a user wants a lightweight-worker Codex pet workflow, a non-pixel custom pet style, a prospect or company mascot pet, or a full 8x9 animated pet atlas with transparent unused cells, QA contact sheets, and pet.json packaging. This skill composes the installed $imagegen system skill for visual generation and uses bundled scripts for deterministic spritesheet assembly.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[853,856,857,860],{"name":854,"slug":855,"type":15},"Animation","animation",{"name":748,"slug":749,"type":15},{"name":858,"slug":859,"type":15},"Creative","creative",{"name":796,"slug":797,"type":15},"2026-05-02T05:31:48.48485",{"slug":863,"name":863,"fn":864,"description":865,"org":866,"tags":867,"stars":715,"repoUrl":716,"updatedAt":877},"imagegen","generate and edit raster images","Generate or edit raster images when the task benefits from AI-created bitmap visuals such as photos, illustrations, textures, sprites, mockups, or transparent-background cutouts. Use when Codex should create a brand-new image, transform an existing image, or derive visual variants from references, and the output should be a bitmap asset rather than repo-native code or vector. Do not use when the task is better handled by editing existing SVG\u002Fvector\u002Fcode-native assets, extending an established icon or logo system, or building the visual directly in HTML\u002FCSS\u002Fcanvas.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[868,869,870,873,876],{"name":858,"slug":859,"type":15},{"name":796,"slug":797,"type":15},{"name":871,"slug":872,"type":15},"Image Generation","image-generation",{"name":874,"slug":875,"type":15},"Images","images",{"name":9,"slug":8,"type":15},"2026-05-15T06:23:24.312127",675,{"items":880,"total":993},[881,897,913,925,943,961,981],{"slug":882,"name":882,"fn":883,"description":884,"org":885,"tags":886,"stars":22,"repoUrl":23,"updatedAt":24},"accessibility-and-inclusive-visualization","make data visualizations accessible","Make data visualizations accessible and inclusive. Use when the user needs chart or diagram accessibility guidance, text alternatives for complex visuals, color and contrast review, keyboard support, reduced-motion behavior for animation or parallax, or an accessibility QA workflow for exported figures, UML-like diagrams, and dashboards.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[887,890,893,896],{"name":888,"slug":889,"type":15},"Accessibility","accessibility",{"name":891,"slug":892,"type":15},"Charts","charts",{"name":894,"slug":895,"type":15},"Data Visualization","data-visualization",{"name":796,"slug":797,"type":15},{"slug":898,"name":898,"fn":899,"description":900,"org":901,"tags":902,"stars":22,"repoUrl":23,"updatedAt":912},"agent-browser","automate browser interactions for agents","Browser automation CLI for AI agents. Use when the user needs to interact with websites, verify dev server output, test web apps, navigate pages, fill forms, click buttons, take screenshots, extract data, or automate any browser task. Also triggers when a dev server starts so you can verify it visually.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[903,906,909],{"name":904,"slug":905,"type":15},"Agents","agents",{"name":907,"slug":908,"type":15},"Browser Automation","browser-automation",{"name":910,"slug":911,"type":15},"Testing","testing","2026-04-06T18:41:03.44016",{"slug":914,"name":914,"fn":915,"description":916,"org":917,"tags":918,"stars":22,"repoUrl":23,"updatedAt":924},"agent-browser-verify","verify dev server output with automated browser","Automated browser verification for dev servers. Triggers when a dev server starts to run a visual gut-check with agent-browser — verifies the page loads, checks for console errors, validates key UI elements, and reports pass\u002Ffail before continuing.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[919,920,923],{"name":907,"slug":908,"type":15},{"name":921,"slug":922,"type":15},"Local Development","local-development",{"name":910,"slug":911,"type":15},"2026-04-06T18:41:17.526867",{"slug":926,"name":926,"fn":927,"description":928,"org":929,"tags":930,"stars":22,"repoUrl":23,"updatedAt":942},"agents-sdk","build AI agents on Cloudflare Workers","Build AI agents on Cloudflare Workers using the Agents SDK. Load when creating stateful agents, durable workflows, real-time WebSocket apps, scheduled tasks, MCP servers, or chat applications. Covers Agent class, state management, callable RPC, Workflows integration, and React hooks. Biases towards retrieval from Cloudflare docs over pre-trained knowledge.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[931,932,933,936,939],{"name":904,"slug":905,"type":15},{"name":764,"slug":765,"type":15},{"name":934,"slug":935,"type":15},"SDK","sdk",{"name":937,"slug":938,"type":15},"Serverless","serverless",{"name":940,"slug":941,"type":15},"WebSockets","websockets","2026-04-06T18:39:51.717063",{"slug":944,"name":944,"fn":945,"description":946,"org":947,"tags":948,"stars":22,"repoUrl":23,"updatedAt":960},"ai-elements","build chat UIs with AI Elements","AI Elements component library guidance — pre-built React components for AI interfaces built on shadcn\u002Fui. Use when building chat UIs, message displays, tool call rendering, streaming responses, reasoning panels, or any AI-native interface with the AI SDK.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[949,950,953,956,957],{"name":801,"slug":802,"type":15},{"name":951,"slug":952,"type":15},"React","react",{"name":954,"slug":955,"type":15},"shadcn\u002Fui","shadcn-ui",{"name":818,"slug":819,"type":15},{"name":958,"slug":959,"type":15},"Vercel","vercel","2026-04-06T18:40:59.619419",{"slug":962,"name":962,"fn":963,"description":964,"org":965,"tags":966,"stars":22,"repoUrl":23,"updatedAt":980},"ai-gateway","configure Vercel AI Gateway","Vercel AI Gateway expert guidance. Use when configuring model routing, provider failover, cost tracking, or managing multiple AI providers through a unified API.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[967,970,973,976,979],{"name":968,"slug":969,"type":15},"AI Infrastructure","ai-infrastructure",{"name":971,"slug":972,"type":15},"Cost Optimization","cost-optimization",{"name":974,"slug":975,"type":15},"LLM","llm",{"name":977,"slug":978,"type":15},"Performance","performance",{"name":958,"slug":959,"type":15},"2026-04-06T18:40:44.377464",{"slug":982,"name":982,"fn":983,"description":984,"org":985,"tags":986,"stars":22,"repoUrl":23,"updatedAt":992},"ai-generation-persistence","implement persistence patterns for AI generations","AI generation persistence patterns — unique IDs, addressable URLs, database storage, and cost tracking for every LLM generation",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[987,988,991],{"name":971,"slug":972,"type":15},{"name":989,"slug":990,"type":15},"Database","database",{"name":974,"slug":975,"type":15},"2026-04-06T18:41:08.513425",600]