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)

code

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):

code

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>
  <circle cx="50" cy="0" r="5" fill="white" stroke="#f97316" stroke-width="2"/>
</g>

Subworkflow Node Template

For workflows containing subworkflows, use a larger card with diagonal stripe pattern:

xml

<g class="subworkflow-card" transform="translate(X, Y)">
  <rect width="280" height="170" rx="6" fill="url(#subworkflow-pattern)" stroke="#25537b" stroke-width="2"/>
  <rect width="280" height="170" rx="6" fill="rgba(255,255,255,0.9)" stroke="#25537b" stroke-width="2"/>
  <!-- Header -->
  <rect width="280" height="32" rx="6" fill="#25537b"/>
  <text x="12" y="22" font-family="system-ui, sans-serif" font-size="14" fill="white">⎔</text>
  <text x="30" y="22" font-family="system-ui, sans-serif" font-size="12" font-weight="700" fill="white">Subworkflow Name</text>
  <!-- Inner content: mini flow diagram, output list -->
</g>

Legend Template

Include a legend at the bottom of the diagram:

xml

<g transform="translate(X, Y)">
  <text x="0" y="0" font-family="system-ui, sans-serif" font-size="10" font-weight="600" fill="#495057">Legend:</text>
  <!-- Input -->
  <rect x="60" y="-10" width="14" height="14" rx="2" fill="white" stroke="#ffd700" stroke-width="1.5"/>
  <text x="80" y="0" font-family="system-ui, sans-serif" font-size="9" fill="#6c757d">Input</text>
  <!-- Data flow -->
  <line x1="120" y1="-4" x2="160" y2="-4" stroke="#25537b" stroke-width="4" stroke-linecap="round"/>
  <text x="168" y="0" font-family="system-ui, sans-serif" font-size="9" fill="#6c757d">Data flow</text>
  <!-- QC metrics -->
  <line x1="240" y1="-4" x2="280" y2="-4" stroke="#25537b" stroke-width="3" stroke-linecap="round" stroke-dasharray="5 3"/>
  <text x="288" y="0" font-family="system-ui, sans-serif" font-size="9" fill="#6c757d">QC metrics</text>
  <!-- Output -->
  <rect x="360" y="-10" width="14" height="14" rx="2" fill="white" stroke="#f97316" stroke-width="1.5"/>
  <text x="380" y="0" font-family="system-ui, sans-serif" font-size="9" fill="#6c757d">Output</text>
  <!-- Report -->
  <rect x="430" y="-10" width="14" height="14" rx="2" fill="white" stroke="#10b981" stroke-width="1.5"/>
  <text x="450" y="0" font-family="system-ui, sans-serif" font-size="9" fill="#6c757d">Report</text>
</g>

Workflow Analysis Process

When given a .ga file:

•
Identify the main spine - The longest path of domain-meaningful steps
•
Classify tools by category:
- •Input (data inputs, not parameters)
- •QC (fastp, FastQC, trimming tools)
- •Mapping (bowtie2, bwa, STAR, HISAT2)
- •Filtering (samtools filter, dedup)
- •Analysis (MACS2, featureCounts, DESeq2, domain-specific tools)
- •Report (MultiQC)
- •Output (workflow outputs)
•
Simplify - Don't show every step:
- •Skip utility steps (format conversion, flatten collection, map_param_value)
- •Skip parameter inputs (quality %, thresholds, boolean flags)
- •Keep data inputs (FASTQs, reference files, GTF annotations)
- •Group repeated similar steps if needed
- •Represent subworkflows as single boxes showing their purpose
•
Layout - Arrange for clarity:
- •Main spine flows left-to-right
- •QC branches curve down to a MultiQC node
- •Outputs positioned below or to the side of final analysis
- •Subworkflows as larger boxes with mini flow diagrams inside

Connection Math

For a connection from output terminal at (x1, y1) to input terminal at (x2, y2):

javascript

// Calculate line shift based on Galaxy's algorithm
const distanceX = Math.abs(x2 - x1);
const distanceY = Math.abs(y2 - y1);
const shift = 15 + (distanceX * 0.15) + (distanceY * 0.08);

// Forward connection (x2 >= x1)
const path = `M ${x1} ${y1} C ${x1 + shift} ${y1}, ${x2 - shift} ${y2}, ${x2} ${y2}`;

// Reverse connection (x2 < x1) - needs extra control points
const lineShiftY = (y2 - y1) / 2;
const path = `M ${x1} ${y1}
  C ${x1 + shift} ${y1}, ${x1 + shift} ${y1 + lineShiftY}, ${x1 + shift} ${y1 + lineShiftY}
  C ${x2 - shift} ${y2 - lineShiftY}, ${x2 - shift} ${y2}, ${x2} ${y2}`;

Critical Rules

•
Connections must connect to terminals - Calculate absolute positions carefully:
- •Node at translate(X, Y) with terminal at cx=CX, cy=CY
- •Absolute terminal position is (X + CX, Y + CY)
•
No animations - Static diagrams only
•
Draw connections BEFORE nodes - So nodes appear on top
•
Include accessibility - role="img", aria-label, <title>, <desc>
•
Keep it simple - Focus on the workflow story, not every detail

Example Workflows

Simple Linear (ChIP-seq style)

code

Input → QC/Trim → Mapping → Filtering → Analysis → Outputs
                                            ↓
                                         MultiQC

Branching (RNA-seq style)

code

Input → QC → Mapping → ┬→ Quantification → Output
                       ├→ Coverage → Output
                       └→ MultiQC

With Subworkflows (End-to-End DE)

code

Sample Sheet → [RNA-seq Processing] → [DE Analysis] → Results
     GTF ────────────┘                      │
                                      Volcano Plot
                                      Heatmaps

Input Modes

•Path to .ga file: workflows/epigenetics/chipseq-pe/chipseq-pe.ga
•Galaxy API URL: https://usegalaxy.org/api/workflows/{id}/download
•Natural language: "ChIP-seq workflow with fastp, bowtie2, MACS2"

Output

Generate a complete, valid SVG file that:

•Can be viewed directly in a browser
•Scales cleanly (vector graphics)
•Matches Galaxy's visual identity
•Tells the workflow's story clearly

Save SVGs to:

•The workflow's directory: workflows/domain/workflow-name/workflow-name-diagram.svg
•Or /tmp/ for review before committing