Cross Track Interchange

Gallery / Feature Showcase

Demonstrates `%%metro interchange:`: parallel tumour/normal lanes share one MarkDuplicates step without merging, drawn as a cross-track interchange so each lane stays straight on its own track instead of pinching together to a point. Auto-layout infers the same interchange for fully-parallel lanes even without the directive.

Mermaid source

%%metro title: Cross-track interchange
%%metro style: dark
%%metro directional: true
%%metro legend: br
%%metro line: tumor | Tumor | #d62728
%%metro line: normal | Normal | #0570b0
%%metro file: fastq_in | FASTQ
%%metro file: out | VCF

%% The two lanes are NOT parallel everywhere: they share a pre-processing trunk
%% (a real convergence), fan out to their own aligners, and merge again at
%% Annotate (a real fan-in, where the lines pinch to a point). MarkDuplicates is
%% the exception -- both lanes run it but never merge there, so it renders as a
%% cross-track interchange that keeps each lane straight on its own track rather
%% than pinching them together. (Auto-layout infers this same interchange even
%% without the directive, since the lanes through MarkDuplicates are parallel;
%% Annotate is left as a convergence because both lanes leave it for one MultiQC.)
%%metro interchange: markduplicates | tumor | normal

graph LR
    subgraph prep [Pre-processing]
        fastq_in[ ]
        fastqc[FastQC]
        fastp[fastp]
        fastq_in -->|tumor,normal| fastqc
        fastqc -->|tumor,normal| fastp
    end

    subgraph calling [Alignment & calling]
        bwa_t[BWA tumour]
        bwa_n[BWA normal]
        markduplicates[MarkDuplicates]
        mutect2[Mutect2]
        haplotypecaller[GATK HC]
        bwa_t -->|tumor| markduplicates
        bwa_n -->|normal| markduplicates
        markduplicates -->|tumor| mutect2
        markduplicates -->|normal| haplotypecaller
    end

    subgraph reporting [Annotation & reporting]
        annotate[VEP]
        multiqc[MultiQC]
        out[ ]
        annotate -->|tumor,normal| multiqc
        multiqc -->|tumor,normal| out
    end

    fastp -->|tumor| bwa_t
    fastp -->|normal| bwa_n
    mutect2 -->|tumor| annotate
    haplotypecaller -->|normal| annotate

CLI command

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

Rendered map