galaxy-workflow-viz

What this skill does

# Galaxy Workflow Visualization

Generate beautiful, static SVG workflow diagrams that match Galaxy's workflow editor visual style.

## When to Use This Skill

Use when:
- Creating visual diagrams for IWC workflow files (in `workflows/` directory)
- Generating workflow overview graphics for documentation
- Building workflow previews for the IWC website (iwc.galaxyproject.org)
- Need a Galaxy-branded visualization of a pipeline

## Relationship to Mermaid Diagrams

This repository already generates Mermaid diagrams via `scripts/create_mermaid.py` - those show the complete step-by-step workflow structure and are useful for detailed technical documentation.

This skill creates **complementary** visualizations that are:
- **Simplified** - Shows the workflow story, not every utility step
- **Branded** - Matches Galaxy's workflow editor visual style
- **Beautiful** - Designed for marketing, landing pages, and quick overviews
- **Hand-crafted** - LLM-generated with human review for quality

## IWC Workflow Locations

Workflows in this repository are organized by domain:
- `workflows/epigenetics/` - ChIP-seq, ATAC-seq, Hi-C
- `workflows/transcriptomics/` - RNA-seq
- `workflows/proteomics/` - Mass spec analysis
- `workflows/computational-chemistry/` - GROMACS, docking
- `workflows/genome-assembly/` - Assembly pipelines
- `workflows/variant-calling/` - SNP/variant detection

Each workflow directory contains a `.ga` file (Galaxy workflow JSON format).

## Visual Style Reference

The output should match Galaxy's actual workflow editor appearance.

### Colors (Galaxy Theme)

```
Primary (brand-primary):     #25537b  - Node headers, connections, borders
Background grid light:       #c5d5e4  - Minor grid lines
Background grid major:       #b0c4d8  - Major grid lines
Canvas background:           #f8f9fa  - Light gray
Input nodes:                 #ffd700  - Gold for workflow data inputs
Output nodes:                #f97316  - Orange for workflow outputs
Report/QC nodes:             #10b981  - Green for MultiQC, reports
Text primary:                #495057  - Body text
Text secondary:              #868e96  - Descriptions, labels
Input node text:             #2C3143  - Dark text on gold background
```

### Node Color Semantics

Use colors to convey meaning at a glance:
- **Gold (#ffd700)**: Data inputs - FASTQs, reference files, GTF annotations, sample sheets
- **Blue (#25537b)**: Processing/analysis steps - the main workflow tools
- **Orange (#f97316)**: Final outputs - the deliverables users care about
- **Green (#10b981)**: QC/Reports - MultiQC, quality summaries

### Node Design

Nodes are Bootstrap-style cards:
- **Width**: ~180-200px for standard nodes
- **Border radius**: 4px
- **Border**: 1px solid #25537b
- **Header**: 28px tall, filled with #25537b, white text
- **Header content**: Step number + tool name (e.g., "2: fastp")
- **Body**: White background, contains description text
- **Drop shadow**: `drop-shadow(1px 2px 3px rgba(0,0,0,0.15))`

### Connection Terminals

- **Standard terminal**: 6px radius circle, white fill, 2px #25537b stroke
- **Small terminal** (QC outputs): 5px radius, 1.5px stroke
- **Position**: At edge of node card (cx=0 for inputs, cx=width for outputs)

### Connection Lines (Bezier "Noodles")

- **Stroke width**: 4px for main flow, 3px for secondary
- **Color**: #25537b (same as nodes)
- **Line cap**: round
- **QC/optional connections**: stroke-dasharray="5 3"
- **Curve style**: Cubic bezier (CSS curveBasis approximation)

Forward connection (left-to-right):
```
M startX startY
C (startX + shift) startY, (endX - shift) endY, endX endY
```

Where `shift = 15 + (distanceX * 0.15) + (distanceY * 0.08)`

## SVG Structure Template

```xml
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 WIDTH HEIGHT" role="img" aria-label="WORKFLOW_NAME workflow diagram">
  <title>WORKFLOW_NAME</title>
  <desc>Brief description of the workflow</desc>

  <defs>
    <!-- Grid pattern -->
    <pattern id="grid" width="20" height="20" patternUnits="userSpaceOnUse">
      <path d="M 20 0 L 0 0 0 20" fill="none" stroke="#c5d5e4" stroke-width="0.5"/>
    </pattern>
    <pattern id="grid-major" width="100" height="100" patternUnits="userSpaceOnUse">
      <rect width="100" height="100" fill="url(#grid)"/>
      <path d="M 100 0 L 0 0 0 100" fill="none" stroke="#b0c4d8" stroke-width="1"/>
    </pattern>

    <style>
      .connection {
        stroke: #25537b;
        stroke-width: 4;
        fill: none;
        stroke-linecap: round;
      }
      .connection-qc {
        stroke: #25537b;
        stroke-width: 3;
        fill: none;
        stroke-linecap: round;
        stroke-dasharray: 5 3;
      }
      .node-card {
        filter: drop-shadow(1px 2px 3px rgba(0,0,0,0.15));
      }
    </style>
  </defs>

  <!-- Background -->
  <rect width="WIDTH" height="HEIGHT" fill="#f8f9fa"/>
  <rect width="WIDTH" height="HEIGHT" fill="url(#grid-major)"/>

  <!-- Title bar -->
  <rect x="0" y="0" width="WIDTH" height="45" fill="#25537b"/>
  <text x="20" y="28" font-family="system-ui, sans-serif" font-size="16" font-weight="600" fill="white">
    WORKFLOW_NAME
  </text>

  <!-- CONNECTIONS (draw first, behind nodes) -->
  <!-- ... bezier paths ... -->

  <!-- NODES -->
  <!-- ... node groups ... -->

  <!-- Legend (optional) -->
</svg>
```

## Node Template (Processing - Blue)

Standard processing/analysis nodes use blue (#25537b):

```xml
<g class="node-card" transform="translate(X, Y)">
  <rect width="200" height="90" rx="4" fill="white" stroke="#25537b" stroke-width="1"/>
  <rect width="200" height="28" rx="4" fill="#25537b"/>
  <rect x="0" y="24" width="200" height="4" fill="#25537b"/>
  <text x="10" y="19" font-family="system-ui, sans-serif" font-size="11" fill="rgba(255,255,255,0.7)">N:</text>
  <text x="26" y="19" font-family="system-ui, sans-serif" font-size="11" font-weight="600" fill="white">Tool Name</text>
  <text x="100" y="55" text-anchor="middle" font-family="system-ui, sans-serif" font-size="10" fill="#495057">Description</text>
  <text x="100" y="72" text-anchor="middle" font-family="system-ui, sans-serif" font-size="9" fill="#868e96">Subtitle</text>
  <!-- Input terminal at left edge -->
  <circle cx="0" cy="45" r="6" fill="white" stroke="#25537b" stroke-width="2"/>
  <!-- Output terminal at right edge -->
  <circle cx="200" cy="45" r="6" fill="white" stroke="#25537b" stroke-width="2"/>
</g>
```

## Input Node Template (Gold header)

Data input nodes use gold (#ffd700) with dark text (#2C3143):

```xml
<g class="node-card" transform="translate(X, Y)">
  <rect width="180" height="90" rx="4" fill="white" stroke="#ffd700" stroke-width="1.5"/>
  <rect width="180" height="28" rx="4" fill="#ffd700"/>
  <rect x="0" y="24" width="180" height="4" fill="#ffd700"/>
  <text x="10" y="19" font-family="system-ui, sans-serif" font-size="11" fill="rgba(44,49,67,0.6)">1:</text>
  <text x="26" y="19" font-family="system-ui, sans-serif" font-size="11" font-weight="600" fill="#2C3143">Input Name</text>
  <text x="90" y="55" text-anchor="middle" font-family="system-ui, sans-serif" font-size="10" fill="#495057">Data type</text>
  <text x="90" y="72" text-anchor="middle" font-family="system-ui, sans-serif" font-size="9" fill="#868e96">Description</text>
  <!-- Output terminal only (inputs have no input terminal) -->
  <circle cx="180" cy="45" r="6" fill="white" stroke="#ffd700" stroke-width="2"/>
</g>
```

## Output Node Template (Orange header)

```xml
<g class="node-card" transform="translate(X, Y)">
  <rect width="100" height="50" rx="4" fill="white" stroke="#f97316" stroke-width="1.5"/>
  <rect width="100" height="20" rx="4" fill="#f97316"/>
  <rect x="0" y="16" width="100" height="4" fill="#f97316"/>
  <text x="50" y="14" text-anchor="middle" font-family="system-ui, sans-serif" font-size="10" font-weight="600" fill="white">Output Name</text>
  <text x="50" y="38" text-anchor="middle" font-family="system-ui, sans-serif" font-size="8" fill="#868e96">format info</text>