docs: modernize workflow diagram to reflect current pipeline capabilities

[kopardev]

Problem

The current workflow diagram (CUTandRUN_Workflow.jpeg) in the documentation is outdated and does not reflect the full range of capabilities available in the CARLISLE pipeline.

Current Pipeline Capabilities Not Shown in Diagram

The diagram should include:

Control Mode Options

• Individual controls (default)
• Pooled controls
• Control-free mode (run_without_controls: false)

Peak Calling Tools (Currently All Available)

• MACS2 (narrow and broad peak calling)
• SEACR (stringent and relaxed)
• GoPeaks (narrow and broad)

Optional Modules (Configurable)

• ROSE: Super-enhancer analysis (run_rose: true/false)
• Differential contrasts: When multiple conditions are provided (run_contrasts: true/false)
• GO enrichment: Functional annotation (run_go_enrichment: true/false)
• Deeptools: Heatmaps, profiles, PCA/correlation plots (deeptools_prep, deeptools_mat, deeptools_heatmap)

Other Details

• Spike-in normalization option (norm_method: "spikein|library|none")
• QC aggregation (FastQC, FastQ Screen, MultiQC)
• Spike-in assessment module

Solution

Create a modernized workflow diagram (Mermaid, PlantUML, or high-quality graphic) that:

1. Shows the core workflow (Cutadapt → Bowtie2 → Filter → Track generation)
2. Displays control mode decision point
3. Shows all three peak callers as options
4. Clearly marks optional modules (with checkboxes or visual indicators)
5. Includes QC pipeline in parallel

Additional Request

@smarches — could you share the ChatGPT prompt you typically use for generating flowchart diagrams? This would help us create a consistent, high-quality diagram that matches the style of other CCBR pipeline documentation.

Labels

• docs
• enhancement