Reconverge Reversed Fold

Gallery / Serpentine Layout

Serpentine-fold reconvergence: a multi-modal pipeline fanning out to stacked analysis sections and reconverging onto a reversed return row.

Mermaid source

examples/topologies/reconverge_reversed_fold.mmd

%%metro title: Reconvergence Reversed Alt
%%metro style: dark
%%metro line: rna | scRNA-seq | #e63946
%%metro line: protein | CITE-seq | #f5c542
%%metro line: atac | scATAC-seq | #457b9d

graph LR
    subgraph preprocessing [Preprocessing]
        pp_input[Input]
        pp_demux[Demux]
        pp_qc_raw[Raw QC]
        pp_trim[Trim]
        pp_filter[Filter]
        pp_qc_clean[Clean QC]
        pp_classify[Classify]
        pp_sort[Sort]

        pp_input -->|rna,atac,protein| pp_demux
        pp_demux -->|rna,atac,protein| pp_qc_raw
        pp_qc_raw -->|rna,atac,protein| pp_trim
        pp_trim -->|rna,atac,protein| pp_filter
        pp_filter -->|rna,atac,protein| pp_qc_clean
        pp_qc_clean -->|rna,atac,protein| pp_classify
        pp_classify -->|rna,atac,protein| pp_sort
    end

    subgraph rna_analysis [RNA Analysis]
        rna_norm[Normalize]
        rna_cluster[Cluster]
        rna_markers[Markers]
        rna_trajectories[Trajectories]
        rna_dge[DGE]

        rna_norm -->|rna| rna_cluster
        rna_cluster -->|rna| rna_markers
        rna_markers -->|rna| rna_trajectories
        rna_trajectories -->|rna| rna_dge
    end

    subgraph atac_analysis [ATAC Analysis]
        atac_peaks[Peak Calling]
        atac_motif[Motif Analysis]
        atac_footprint[Footprinting]
        atac_coverage[Coverage]

        atac_peaks -->|atac| atac_motif
        atac_motif -->|atac| atac_footprint
        atac_footprint -->|atac| atac_coverage
    end

    subgraph protein_analysis [Protein Analysis]
        prot_norm[Normalize]
        prot_quant[Quantify]
        prot_viz[Visualize]

        prot_norm -->|protein| prot_quant
        prot_quant -->|protein| prot_viz
    end

    subgraph integration [Multi-Modal Integration]
        int_merge[Merge Modalities]
        int_wnn[WNN]
        int_umap[UMAP]

        int_merge -->|rna,atac,protein| int_wnn
        int_wnn -->|rna,atac,protein| int_umap
    end

    subgraph bio_interp [Biological Interpretation]
        bio_celltype[Cell Typing]
        bio_trajectory[Trajectory]
        bio_grn[Gene Reg. Network]

        bio_celltype -->|rna,atac| bio_trajectory
        bio_trajectory -->|rna,atac| bio_grn
    end

    subgraph tech_qc [Technical QC]
        tqc_doublet[Doublet Detection]
        tqc_ambient[Ambient RNA]
        tqc_metrics[QC Metrics]

        tqc_doublet -->|protein| tqc_ambient
        tqc_ambient -->|protein| tqc_metrics
    end

    subgraph final_report [Final Report]
        fr_aggregate[Aggregate]
        fr_report[Render Report]

        fr_aggregate -->|rna,atac,protein| fr_report
    end

    pp_sort -->|rna| rna_norm
    pp_sort -->|atac| atac_peaks
    pp_sort -->|protein| prot_norm
    rna_dge -->|rna| int_merge
    atac_coverage -->|atac| int_merge
    prot_viz -->|protein| int_merge
    int_umap -->|rna,atac| bio_celltype
    int_umap -->|protein| tqc_doublet
    bio_grn -->|rna,atac| fr_aggregate
    tqc_metrics -->|protein| fr_aggregate

CLI command

nf-metro render examples/topologies/reconverge_reversed_fold.mmd -o reconverge_reversed_fold.svg

Rendered map