895 件 ・ 関連度順
概要と使いどころ
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.
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。
Execute ENCODE DNase-seq pipeline from FASTQ to hotspots and footprints. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing DNase-seq data, calling DNase hypersensitive sites, performing footprinting analysis. Trigger on: DNase-seq pipeline, DNase hypersensitive, DHS, Hotspot2, footprinting, DNase I, chromatin accessibility DNase.
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。
Use when designing nonprofit fundraising lifecycle stages, donor pipeline workflows, cultivation-to-stewardship cycles, or Salesforce Opportunity sales process configuration for NPSP or Nonprofit Cloud. Trigger keywords: fundraising lifecycle, donor pipeline, cultivation stage, solicitation workflow, major gift process, moves management, NPSP Opportunity stages, stewardship cycle, NPC fundraising stages. NOT for lapsed donor re-engagement or portfolio segmentation — use admin/donor-lifecycle-requirements. NOT for Engagement Plan setup — use admin/npsp-engagement-plans.
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。
Git branching strategies, conflict resolution, rebase workflows, monorepo patterns, and advanced operations like cherry-pick, bisect, and reflog recovery. Activate on "git", "branching strategy", "merge conflict", "rebase", "cherry-pick", "monorepo git", "git bisect", "git reflog", "squash commits". NOT for GitHub Actions CI/CD (use github-actions-pipeline-builder), GitHub API/webhooks, or PR review processes (use code-review-checklist).
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。
Expert data engineer for ETL/ELT pipelines, streaming, data warehousing. Activate on: data pipeline, ETL, ELT, data warehouse, Spark, Kafka, Airflow, dbt, data modeling, star schema, streaming data, batch processing, data quality. NOT for: API design (use api-architect), ML training (use ML skills), dashboards (use design skills).
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。
Build Sankey, alluvial, river, and CONSORT-style flow diagrams to visualize cohort transitions, cell-state changes, or pipeline filtering using ggalluvial, networkD3, plotly, and consort. Use when showing how entities move between categories across timepoints (cell states, drug response classes, patient flow through a trial) or filtering pipelines (variants filtered through QC stages).
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。
Call copy number variants with the GATK best-practices workflows — the somatic CNV pipeline (CollectReadCounts, DenoiseReadCounts with tangent normalization, ModelSegments, CallCopyRatioSegments) and the germline GATK-gCNV pipeline (DetermineGermlineContigPloidy, GermlineCNVCaller cohort/case mode, PostprocessGermlineCNVCalls). Covers panel-of-normals construction, AnnotateIntervals/FilterIntervals, allelic-count integration, and QS-based filtering. Use when integrating CNV calling into a GATK variant pipeline, calling rare germline CNVs from an exome cohort, deciding between the somatic and germline GATK workflows, or diagnosing why tangent normalization removed a real event or why gCNV output has low precision.
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。
结构化的6步骤流程，用于改进、改造或重构现有的流水线（pipeline）、独立项目文件夹、文档结构或软件技术栈。可调用为“pipeline optimizer”（针对整个主题流水线，例如软件、研究或游戏开发流水线）或“project-folder optimizer”（针对流水线内的独立项目文件夹，例如单个软件工具或论文项目）。触发于诸如“改进流水线X”、“优化技术栈”、“重构Y”、“改造”、“流水线重构”、“清理项目文件夹”、“改进文件夹结构”、“统一规范”、“文档整合”、“集成到现有系统”或针对既有结构的任何实质性干预等任务。提供既有资产调查、目的明确化、理想蓝图草图、差距规划、实证痛点识别以及使用全新的子智能体进行重新测试。防止并行标准、重复建设和流水线中断。
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。
既存のパイプライン、個別プロジェクトフォルダ、ドキュメント構造、またはソフトウェアスタックを改善、改修、再構築するための構造化された6ステップのプロシージャ。「pipeline optimizer」（ソフトウェア、研究、ゲーム開発パイプラインなど、トピック全体のパイプライン対象）または「project-folder optimizer」（単一のソフトウェアツールや論文プロジェクトなど、パイプライン内の個別プロジェクトフォルダ対象）として呼び出し可能。「パイプラインXを改善する」、「スタックを最適化する」、「Yを再構築する」、「改修」、「パイプラインのリファクタリング」、「プロジェクトフォルダのクリーンアップ」、「フォルダ構造の改善」、「規約の統一」、「ドキュメントの統合」、「既存システムへの統合」、または確立された構造に対する実質的な介入タスクで起動。既存資産の調査、目的の明確化、理想像のスケッチ、ギャップ計画、経験的課題の特定、および新しいサブエージェントによる再テストを提供。並行標準の発生、重複、パイプラインの破綻を防止。
Build production Apache Airflow DAGs with best practices for operators, sensors, testing, and deployment. Use when creating data pipelines, orchestrating workflows, or scheduling batch jobs.
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。
Build end-to-end MLOps pipelines from data preparation through model training, validation, and production deployment. Use when creating ML pipelines, implementing MLOps practices, or automating model training and deployment workflows.
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。
Use when working with Dagger — dagger CI/CD pipeline management. Covers pipeline-as-code configuration, module management, function execution, caching layers, container builds, and pipeline debugging. Use when managing Dagger pipelines, debugging function execution, inspecting modules, or optimizing container-based CI workflows.
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。
Set up a complete CI/CD pipeline for a project. Detects the stack, then generates and validates GitHub Actions workflows, a Dockerfile, and a Makefile as one coherent pipeline. Use when asked to "set up CI", "add pipeline", "create GitHub Actions", "ci/cd setup", "automate builds", "containerize", or "add a Makefile".
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。
Create polished, validated architecture, workflow, sequence, data-flow, and lifecycle/state diagrams as explorable standalone HTML with inline SVG, dark/light themes, optional trace motion, and PNG/JPEG/WebP/SVG/WebM export. Accept plain-language requirements or pasted Mermaid flowchart, sequenceDiagram, and stateDiagram input; inspect repository evidence when the diagram must reflect real code. Use when the user asks to visualize system architecture, infrastructure, cloud/security/network topology, technical workflows, API call sequences, request lifecycles, data pipelines, ETL/ELT, data lineage, state machines, or to convert/beautify Mermaid.
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。
Diagnoses CI and pull-request pipeline health for a GitHub repo using the engineering analytics MCP tools — pull-requests (PR list with CI status), workflow-health (per-workflow CI trends), and pr-lifecycle (a single PR's timeline). Use when asked whether CI is getting faster or slower, which GitHub Actions workflow is the slow or flaky long-pole, how long PRs take from open to merge, how an author's merge time compares to the cohort, which open PRs have failing or pending CI, or where a specific pull request is stuck. Triggers on "engineering analytics", "is CI getting slower", "slow workflow", "flaky CI", "time to merge", "cycle time", "PR throughput", "failing checks", "where is PR <n> stuck", "CI long pole", "what's holding up this PR".
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。
Build Sankey, alluvial, river, and CONSORT-style flow diagrams to visualize cohort transitions, cell-state changes, or pipeline filtering using ggalluvial, networkD3, plotly, and consort. Use when showing how entities move between categories across timepoints (cell states, drug response classes, patient flow through a trial) or filtering pipelines (variants filtered through QC stages).
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。
Authors reproducible bioinformatics pipelines with Snakemake - rules wired by output-file pattern, wildcards and expand() for sample fan-out, checkpoints for runtime-unknown outputs, resource/retry escalation, and conda/container software deployment on HPC and cloud. Use when deciding rule-based (Snakemake) vs channel/dataflow (Nextflow) authoring; wiring rules by OUTPUT-file pattern rather than imperative order; using wildcards + expand() for sample fan-out and constraining them to stop silent mis-routing; adding checkpoints when the set of outputs is unknown until a step runs (dynamic DAG); diagnosing why a job reran (or did not) under the mtime-plus-provenance trigger set; escalating memory on retry for OOM-killed jobs; and porting a Snakemake 7 `--cluster`/remote-provider command to the Snakemake 8+ executor-plugin and storage-plugin model (snakemake-executor-plugin-slurm) with `--software-deployment-method`.
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。
Authors bioinformatics pipelines in WDL (Workflow Description Language) run by Cromwell or miniwdl, targeting the GATK/Broad and Terra/AnVIL/BioData Catalyst cloud ecosystem, with tasks, workflows, scatter-gather parallelism, structs, and a runtime block that sizes the cloud VM. Use when deciding to target Terra/AnVIL/GATK/WARP (chosen for the ecosystem, not the language); sizing runtime disks dynamically for a fresh-per-task cloud VM (ceil(size(f)*factor)+buffer); choosing preemptible vs on-demand VMs by task length and idempotency; picking Cromwell (production, cloud, call-caching) vs miniwdl (local dev, miniwdl check linting, readable errors); enabling and debugging call-caching silent-miss modes; pinning Docker by digest for reproducibility and cache stability; or scattering an array for parallel fan-out.
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。
End-to-end 16S/ITS amplicon workflow from demultiplexed FASTQ to a consensus differential-abundance result, orchestrating cutadapt primer removal, per-run DADA2 ASV inference (learnErrors/mergeSequenceTables/removeBimeraDenovo), region-matched taxonomy assignment, a SEPP/Greengenes2 tree, alpha/beta diversity at a declared sampling depth (phyloseq/vegan, adonis2 paired with betadisper), compositional DA as a consensus of >=2 tools (ALDEx2/ANCOM-BC2) on unrarefied counts, and optional PICRUSt2 functional prediction gated on NSTI. Covers the stage-ordering decisions (primers before truncation, per-run error model, rarefy for diversity not DA, predicted potential not activity) and defers each per-step choice to the six microbiome skills. Use when staging an amplicon study end to end or chaining ASV inference, taxonomy, diversity, and differential abundance. For shotgun reads see workflows/metagenomics-pipeline.
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。
Build Sankey, alluvial, river, and CONSORT-style flow diagrams to visualize cohort transitions, cell-state changes, or pipeline filtering using ggalluvial, networkD3, plotly, and consort. Use when showing how entities move between categories across timepoints (cell states, drug response classes, patient flow through a trial) or filtering pipelines (variants filtered through QC stages).
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。
Call copy number variants with the GATK best-practices workflows — the somatic CNV pipeline (CollectReadCounts, DenoiseReadCounts with tangent normalization, ModelSegments, CallCopyRatioSegments) and the germline GATK-gCNV pipeline (DetermineGermlineContigPloidy, GermlineCNVCaller cohort/case mode, PostprocessGermlineCNVCalls). Covers panel-of-normals construction, AnnotateIntervals/FilterIntervals, allelic-count integration, and QS-based filtering. Use when integrating CNV calling into a GATK variant pipeline, calling rare germline CNVs from an exome cohort, deciding between the somatic and germline GATK workflows, or diagnosing why tangent normalization removed a real event or why gCNV output has low precision.
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。
Helps understand and write EAS workflow YAML files for Expo projects. Use this skill when the user asks about CI/CD or workflows in an Expo or EAS context, mentions .eas/workflows/, or wants help with EAS build pipelines or deployment automation.
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。
Build Sankey, alluvial, river, and CONSORT-style flow diagrams to visualize cohort transitions, cell-state changes, or pipeline filtering using ggalluvial, networkD3, plotly, and consort. Use when showing how entities move between categories across timepoints (cell states, drug response classes, patient flow through a trial) or filtering pipelines (variants filtered through QC stages).
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。
Call copy number variants with the GATK best-practices workflows — the somatic CNV pipeline (CollectReadCounts, DenoiseReadCounts with tangent normalization, ModelSegments, CallCopyRatioSegments) and the germline GATK-gCNV pipeline (DetermineGermlineContigPloidy, GermlineCNVCaller cohort/case mode, PostprocessGermlineCNVCalls). Covers panel-of-normals construction, AnnotateIntervals/FilterIntervals, allelic-count integration, and QS-based filtering. Use when integrating CNV calling into a GATK variant pipeline, calling rare germline CNVs from an exome cohort, deciding between the somatic and germline GATK workflows, or diagnosing why tangent normalization removed a real event or why gCNV output has low precision.
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。