Marker Styles

Gallery / Feature Showcase

Per-station marker shapes & fills encoding tool attributes (mandatory/optional/accelerated/expanded-elsewhere) with a marker key alongside the line legend. Demonstrates `%%metro marker:` and `%%metro marker_legend:`.

Mermaid source

examples/marker_styles.mmd

%%metro title: Per-station marker styles
%%metro style: dark
%%metro line: germline | Germline calling | #0570b0
%%metro line: somatic | Somatic calling | #e63946
%%metro legend: bl

%% Per-station marker shapes & fills: square = mandatory, circle = optional,
%% coloured square = hardware-accelerated, pill = a step whose detail is
%% expanded in a separate panel.
%%metro marker: bwa | square, solid
%%metro marker: markdup | square, solid
%%metro marker: bqsr | square, #4CAF50
%%metro marker: haplotypecaller | square, #4CAF50
%%metro marker: mutect2 | square, #1f4e79
%%metro marker: cnvkit | pill, open
%%metro marker: vep | circle, open
%%metro marker: snpeff | circle, open

%% Marker key captions.
%%metro marker_legend: square, solid | Mandatory
%%metro marker_legend: circle, open | Optional
%%metro marker_legend: pill, open | Expanded elsewhere
%%metro marker_legend: square, #4CAF50 | Parabricks accelerated
%%metro marker_legend: square, #1f4e79 | Sentieon accelerated

graph LR
    subgraph alignment [Alignment & preprocessing]
        bwa[BWA-MEM]
        markdup[MarkDuplicates]
        bqsr[BQSR]

        bwa -->|germline,somatic| markdup
        markdup -->|germline,somatic| bqsr
    end

    subgraph calling [Variant calling & annotation]
        haplotypecaller[HaplotypeCaller]
        mutect2[Mutect2]
        cnvkit[CNVkit]
        snpeff[SnpEff]
        vep[VEP]

        haplotypecaller -->|germline| snpeff
        mutect2 -->|somatic| vep
        mutect2 -->|somatic| cnvkit
    end

    %% Inter-section edges
    bqsr -->|germline| haplotypecaller
    bqsr -->|somatic| mutect2

CLI command

nf-metro render examples/marker_styles.mmd -o marker_styles.svg

Rendered map