Results for “scratch”

Runs and configures curated nf-core community Nextflow pipelines (rnaseq, sarek, atacseq, methylseq, ampliseq, taxprofiler, fetchngs) reproducibly, pinning the pipeline revision with -r and selecting a container engine and institutional config via -profile. Use when deciding to adopt a community pipeline versus author one from scratch; picking a pipeline and pinning its -r revision; selecting -profile test/docker/singularity/conda plus an institutional config from nf-core/configs; building and validating a samplesheet CSV against the pipeline schema (nf-schema); choosing --genome/iGenomes versus custom references; configuring resources and max_memory for SLURM/AWS Batch; using -resume and -stub; and reading MultiQC outputs.

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Authors reproducible Nextflow DSL2 pipelines built on reactive dataflow, where processes communicate only through channels and execution order is not guaranteed. Use when deciding channel/dataflow (Nextflow) vs rule-based (Snakemake) authoring; wiring queue vs value channels and fixing shared-reference exhaustion with .first(); composing DSL2 modules and subworkflows with take/main/emit; selecting container/conda profiles and pinning images by digest for portability across local/SLURM/LSF/AWS Batch/Google Batch/Kubernetes executors; diagnosing why -resume misses the cache (nondeterministic input order, mtime on network filesystems, mutable :latest tags) with cache 'lenient' and -dump-hashes; managing work/ vs publishDir and dynamic retry escalation; and choosing whether to adopt an nf-core community pipeline or author from scratch.

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Scaffold a minimal GNOME-compliant GTK4/libadwaita app from scratch — window, header bar, ViewSwitcher, adaptive breakpoint, menu, preferences, GSettings schema, desktop entry, meson. Use when starting a new GNOME app or when the user asks for a GNOME app template.

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Build an animation from scratch, making the decisions in the order that determines whether it feels right — should it animate at all, what purpose, which tool, which properties, which curve and duration, how it interrupts, how it exits. Writes the implementation. Use when asked to animate something, add motion, make a component feel alive, or build a transition. For critiquing existing motion use review-animations; for auditing a whole codebase use improve-animations.

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Rust 製 AI/ML ライブラリ fandhe-ai のリファレンス。Burn / candle / tch 非依存の from-scratch 実装。 tape(), tape_for, Tape, Gradients, Tensor, Var, LinearVars, autodiff, kernel fusion, FusionPlan, BackendOps, Device (Cpu / Cuda / Metal), DeviceParamStore, compat::array, compat::Sequential, nn::Module, optim (AdamW / GradScaler), data::DataLoader, ONNX import / export, safetensors, inference::generate / KvCache, guardrail / self-repair CLI。

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Download raw sequencing reads from NCBI SRA using sra-tools (prefetch, fasterq-dump, vdb-validate) or the ENA mirror. Use when pulling FASTQ for SRR/ERR/DRR accessions, deciding between SRA-direct, ENA mirror, or AWS/GCP cloud mirror (STRIDES), handling --include-technical for 10x and other single-cell records, validating with MD5/vdb-validate, navigating SRR/SRX/SRS/SRP/PRJNA hierarchy, or finding accessions via pysradb. Encodes SRA cloud-egress economics, the fasterq-dump uncompressed-scratch trap, and the --max-size default that silently truncates large prefetches.

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Build publication-quality figures with matplotlib using the object-oriented Figure/Axes API, constrained_layout, rcParams customization, TrueType (Type-42) font embedding for journal submission, and CVD-safe palettes. Covers seaborn integration, common chart types, axis formatting, and the small gotchas that distinguish reproducible matplotlib from notebook scratch. Use when producing publication figures in Python — RNA-seq scatter, single-cell embeddings, generic biological plotting.

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Create new skills, modify and improve existing skills, and measure skill performance. Use when users want to create a skill from scratch, edit, or optimize an existing skill, run evals to test a skill, benchmark skill performance with variance analysis, or optimize a skill's description for better triggering accuracy.

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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, .xltx, .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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Create new skills, modify and improve existing skills, and measure skill performance. Use when users want to create a skill from scratch, edit, or optimize an existing skill, run evals to test a skill, benchmark skill performance with variance analysis, or optimize a skill's description for better triggering accuracy.

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Review or refactor an existing SKILL.md and its bundled resources — a smaller always-loaded core, conditional references, preserved behavior, lean/guided consumer profiles, and an A/B protocol to compare a candidate with the previous version. Use when a skill repeats itself, loads references on every run, triggers too broadly or misses legitimate requests, or needs its efficiency measured across models. Do NOT use for writing a new skill from scratch, refactoring application code, translating a skill verbatim, or performing the target skill's own task.

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When the user wants to edit, review, or improve existing marketing copy. Also use when the user mentions 'edit this copy,' 'review my copy,' 'copy feedback,' 'proofread,' 'polish this,' 'make this better,' 'copy sweep,' 'tighten this up,' 'this reads awkwardly,' 'clean up this text,' 'too wordy,' or 'sharpen the messaging.' Use this when the user already has copy and wants it improved rather than rewritten from scratch. For writing new copy, see copywriting.

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Design finalization: generates production-quality Pretext-native HTML/CSS. Works with approved mockups from /design-shotgun, CEO plans from /plan-ceo-review, design review context from /plan-design-review, or from scratch with a user description. Text actually reflows, heights are computed, layouts are dynamic. 30KB overhead, zero deps. Smart API routing: picks the right Pretext patterns for each design type. Use when: "finalize this design", "turn this into HTML", "build me a page", "implement this design", or after any planning skill. Proactively suggest when user has approved a design or has a plan ready. (gstack) Voice triggers (speech-to-text aliases): "build the design", "code the mockup", "make it real".

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Creates a new AEM Edge Delivery site from scratch — GitHub repo from the boilerplate, aem-code-sync installation, initial DA content (nav, footer, homepage), and a live preview URL. Use this skill whenever a user wants to create a new AEM Edge Delivery site and no repository or DA content exists yet.

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Strip a problem to its irreducible fundamental truths and rebuild the solution from the ground up — free from analogy, convention, and inherited assumptions. Load when the user feels constrained by how something has always been done, when existing solutions feel expensive or inefficient for no good reason, when the user asks to think from first principles, challenge the fundamentals, or rebuild this from scratch. Also triggers on "why does it have to work this way", "what are the actual constraints here", "ignore what everyone else does", or when deep-thinking diagnoses a convention-break frame. Based on Aristotle's first principles method, popularised by Musk and Feynman. Produces genuinely novel solutions by eliminating convention.

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Create stunning, animation-rich HTML presentations from scratch or by converting PowerPoint files. Use when the user wants to build a presentation, convert a PPT/PPTX to web, or create slides for a talk/pitch. Helps non-designers discover their aesthetic through visual exploration rather than abstract choices.

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Download raw sequencing reads from NCBI SRA using sra-tools (prefetch, fasterq-dump, vdb-validate) or the ENA mirror. Use when pulling FASTQ for SRR/ERR/DRR accessions, deciding between SRA-direct, ENA mirror, or AWS/GCP cloud mirror (STRIDES), handling --include-technical for 10x and other single-cell records, validating with MD5/vdb-validate, navigating SRR/SRX/SRS/SRP/PRJNA hierarchy, or finding accessions via pysradb. Encodes SRA cloud-egress economics, the fasterq-dump uncompressed-scratch trap, and the --max-size default that silently truncates large prefetches.

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Build publication-quality figures with matplotlib using the object-oriented Figure/Axes API, constrained_layout, rcParams customization, TrueType (Type-42) font embedding for journal submission, and CVD-safe palettes. Covers seaborn integration, common chart types, axis formatting, and the small gotchas that distinguish reproducible matplotlib from notebook scratch. Use when producing publication figures in Python — RNA-seq scatter, single-cell embeddings, generic biological plotting.

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Guides the practical path from 'we have no design system' or 'we have a mess' to a real, functional design system. Component inventory, design token extraction, headless UI adoption (Radix, React Aria, Headless UI), migration order of operations, and the assessment-to-rollout pipeline. Activate on 'design system from scratch', 'bootstrap design system', 'no design system', 'design system migration', 'headless UI adoption', 'component audit', 'design token extraction', 'design system strategy'. NOT for building specific components once a system exists (use design-system-creator), not for generating token files/configs (use design-system-generator).

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Interprets GitHub Actions run status and logs, diagnoses CI failure patterns, and suggests targeted fixes. Handles dependency install failures, test timeouts, build OOM, flaky tests, and workflow misconfigurations. Activate on: 'CI failing', 'build broken', 'workflow error', 'GitHub Actions debug', 'flaky CI', 'pipeline timeout', 'CI red'. NOT for: writing new workflows from scratch (use github-actions-pipeline-builder), CI caching strategy (use ci-cache-optimizer), deployment orchestration (use devops-automator).

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Build, debug, optimize, and deploy ComfyUI workflows for diffusion image, video, and audio generation. Activate on: ComfyUI workflow, ComfyUI custom node, ComfyUI API, ComfyUI Manager, KSampler, FLUX in ComfyUI, Wan 2.2 ComfyUI, Hunyuan video ComfyUI, LTX video ComfyUI, IPAdapter, ControlNet ComfyUI, Kijai wrapper, ComfyDeploy, RunComfy, ComfyUI security, GGUF quantization, TeaCache, Nunchaku, ACE-Step ComfyUI, F5-TTS ComfyUI, subgraphs ComfyUI. NOT for: A1111/Forge/Invoke (different UIs), training pipelines from scratch, non-diffusion ML models, or general image-API integrations (use generative-video-2026 / generative-music-audio / media-gen-deployment).

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Generates OpenAPI 3.0/3.1 specs, TypeScript client types, and curl examples from existing route handler code. Supports Express, Next.js API routes, Fastify, and Hono. Produces complete documentation including auth requirements, rate limits, error codes, and request/response examples. Activate on: 'generate API docs', 'OpenAPI from code', 'document endpoints', 'API reference', 'swagger generation', 'endpoint documentation'. NOT for: API design from scratch (use api-architect), deployment (use devops-automator), testing (use test-automation-expert).

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Build or improve a Coval dashboard with metric visualizations backed by real data. Creates new dashboards from scratch or rebuilds existing ones by analyzing usage patterns, metric frequency, and data density. Use when user says "create a dashboard", "build a dashboard", "improve my dashboard", "add widgets", "visualize my metrics", "make a performance dashboard", or "dashboard for my runs".

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Reimagine UI posture — bold from-scratch reinvention of a screen. Use when asked to rethink or reinvent a UI, merge screens, change its core interaction model, break the frame rather than polish, or generate surprising new concepts.

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