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claude-scientific-skills/scientific-skills/markdown-mermaid-writing/references/diagrams/flowchart.md
Clayton Young ea5a287cf9 fix(attribution): correct source repo URL to SuperiorByteWorks-LLC/agent-project
All 40 references to borealBytes/opencode updated to the correct source:
https://github.com/SuperiorByteWorks-LLC/agent-project

Affected files: SKILL.md, all 24 diagram guides, 9 templates, issue and PR
docs, plus assets/examples/example-research-report.md (new file).

The example report demonstrates full skill usage: flowchart, sequence,
timeline, xychart, radar diagrams — all with accTitle/accDescr and
classDef colors, no %%{init}. Covers HEK293T CRISPR editing efficiency
as a realistic scientific context.
2026-02-23 07:43:04 -05:00

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Flowchart

Back to Style Guide — Read the style guide first for emoji, color, and accessibility rules.

Syntax keyword: flowchart Best for: Sequential processes, workflows, decision logic, troubleshooting trees When NOT to use: Complex timing between actors (use Sequence), state machines (use State)


Exemplar Diagram

flowchart TB
    accTitle: Feature Development Lifecycle
    accDescr: End-to-end feature flow from idea through design, build, test, review, and release with a revision loop on failed reviews

    idea([💡 Feature idea]) --> spec[📋 Write spec]
    spec --> design[🎨 Design solution]
    design --> build[🔧 Implement]
    build --> test[🧪 Run tests]
    test --> review{🔍 Review passed?}
    review -->|Yes| release[🚀 Release to prod]
    review -->|No| revise[✏️ Revise code]
    revise --> test
    release --> monitor([📊 Monitor metrics])

    classDef start fill:#ede9fe,stroke:#7c3aed,stroke-width:2px,color:#3b0764
    classDef process fill:#dbeafe,stroke:#2563eb,stroke-width:2px,color:#1e3a5f
    classDef decision fill:#fef9c3,stroke:#ca8a04,stroke-width:2px,color:#713f12
    classDef success fill:#dcfce7,stroke:#16a34a,stroke-width:2px,color:#14532d

    class idea,monitor start
    class spec,design,build,test,revise process
    class review decision
    class release success

Tips

  • Use TB (top-to-bottom) for processes, LR (left-to-right) for pipelines
  • Rounded rectangles ([text]) for start/end, diamonds {text} for decisions
  • Max 10 nodes — split larger flows into "Phase 1" / "Phase 2" diagrams
  • Max 3 decision points per diagram
  • Edge labels should be 14 words: -->|Yes|, -->|All green|
  • Use classDef for semantic coloring — decisions in amber, success in green, actions in blue

Subgraph Pattern

When you need grouped stages:

flowchart TB
    accTitle: CI/CD Pipeline Stages
    accDescr: Three-stage pipeline grouping code quality checks, testing, and deployment into distinct phases

    trigger([⚡ Push to main])

    subgraph quality ["🔍 Code Quality"]
        lint[📝 Lint code] --> format[⚙️ Check formatting]
    end

    subgraph testing ["🧪 Testing"]
        unit[🧪 Unit tests] --> integration[🔗 Integration tests]
    end

    subgraph deploy ["🚀 Deployment"]
        build[📦 Build artifacts] --> ship[☁️ Deploy to staging]
    end

    trigger --> quality
    quality --> testing
    testing --> deploy
    deploy --> done([✅ Pipeline complete])

    classDef trigger_style fill:#ede9fe,stroke:#7c3aed,stroke-width:2px,color:#3b0764
    classDef success fill:#dcfce7,stroke:#16a34a,stroke-width:2px,color:#14532d

    class trigger trigger_style
    class done success

Template

flowchart TB
    accTitle: Your Title Here (3-8 words)
    accDescr: One or two sentences explaining what this diagram shows and what insight the reader gains

    start([🏁 Starting point]) --> step1[⚙️ First action]
    step1 --> decision{🔍 Check condition?}
    decision -->|Yes| step2[✅ Positive path]
    decision -->|No| step3[🔧 Alternative path]
    step2 --> done([🏁 Complete])
    step3 --> done

Complex Example

A 20+ node e-commerce order pipeline organized into 5 subgraphs, each representing a processing phase. Subgraphs connect through internal nodes, decision points route orders to exception handling, and color classes distinguish phases at a glance.

flowchart TB
    accTitle: E-Commerce Order Processing Pipeline
    accDescr: Full order lifecycle from intake through fulfillment, shipping, and notification with exception handling paths for payment failures, stockouts, and delivery issues

    order_in([📥 New order]) --> validate_pay{💰 Payment valid?}

    subgraph intake ["📥 Order Intake"]
        validate_pay -->|Yes| check_fraud{🔐 Fraud check}
        validate_pay -->|No| pay_fail[❌ Payment **declined**]
        check_fraud -->|Clear| check_stock{📦 In stock?}
        check_fraud -->|Flagged| manual_review[🔍 Manual **review**]
        manual_review --> check_stock
    end

    subgraph fulfill ["📦 Fulfillment"]
        pick[📋 **Pick** items] --> pack[📦 Pack order]
        pack --> label[🏷️ Generate **shipping** label]
    end

    subgraph ship ["🚚 Shipping"]
        handoff[🚚 Carrier **handoff**] --> transit[📍 In transit]
        transit --> deliver{✅ Delivered?}
    end

    subgraph notify ["📤 Notifications"]
        confirm_email[📧 Order **confirmed**]
        ship_update[📧 Shipping **update**]
        deliver_email[📧 Delivery **confirmed**]
    end

    subgraph exception ["⚠️ Exception Handling"]
        pay_fail --> retry_pay[🔄 Retry payment]
        retry_pay --> validate_pay
        out_of_stock[📦 **Backorder** created]
        deliver_fail[🔄 **Reattempt** delivery]
    end

    check_stock -->|Yes| pick
    check_stock -->|No| out_of_stock
    label --> handoff
    deliver -->|Yes| deliver_email
    deliver -->|No| deliver_fail
    deliver_fail --> transit

    check_stock -->|Yes| confirm_email
    handoff --> ship_update
    deliver_email --> complete([✅ Order **complete**])

    classDef intake_style fill:#dbeafe,stroke:#2563eb,stroke-width:2px,color:#1e3a5f
    classDef fulfill_style fill:#ede9fe,stroke:#7c3aed,stroke-width:2px,color:#3b0764
    classDef ship_style fill:#dcfce7,stroke:#16a34a,stroke-width:2px,color:#14532d
    classDef warn_style fill:#fef9c3,stroke:#ca8a04,stroke-width:2px,color:#713f12
    classDef danger_style fill:#fee2e2,stroke:#dc2626,stroke-width:2px,color:#7f1d1d

    class validate_pay,check_fraud,check_stock,manual_review intake_style
    class pick,pack,label fulfill_style
    class handoff,transit,deliver ship_style
    class confirm_email,ship_update,deliver_email warn_style
    class pay_fail,retry_pay,out_of_stock,deliver_fail danger_style

Why this works

  • 5 subgraphs map to real business phases — intake, fulfillment, shipping, notification, and exceptions are how operations teams actually think about orders
  • Exception handling is its own subgraph — not scattered across phases. Agents and readers can see all failure paths in one place
  • Color classes reinforce structure — blue for intake, purple for fulfillment, green for shipping, amber for notifications, red for exceptions. Even without reading labels, the color pattern tells you which phase you're looking at
  • Decisions route between subgraphs — the diamonds ({Payment valid?}, {In stock?}, {Delivered?}) are the points where flow branches, and each branch leads to a clearly-labeled destination