Gallery

Examples covering the full range of layout patterns.

Getting Started

Feature Showcase

Opt-in static flow chevrons via `%%metro directional: true` (CLI: `--directional`): periodic open chevrons ride each route pointing source to target. A three-line bundled trunk fans out to per-line analyses and converges again, so the chevrons make bundle, fan-out, and merge direction legible without the animated `--animate` balls. Marker size, spacing, opacity, and colour are `Theme` knobs.

Mermaid source

%%metro title: Directional Flow
%%metro style: dark
%%metro directional: true
%%metro line: dna | DNA variants | #E64A19
%%metro line: rna | RNA expression | #1E88E5
%%metro line: meth | Methylation | #43A047

graph LR
    reads[Reads]
    qc[QC]
    trim[Trim]
    align[Align]
    callvar[Call variants]
    quant[Quantify]
    methcall[Call methylation]
    report[Report]

    reads -->|dna| qc
    reads -->|rna| qc
    reads -->|meth| qc
    qc -->|dna| trim
    qc -->|rna| trim
    qc -->|meth| trim
    trim -->|dna| align
    trim -->|rna| align
    trim -->|meth| align
    align -->|dna| callvar
    align -->|rna| quant
    align -->|meth| methcall
    callvar -->|dna| report
    quant -->|rna| report
    methcall -->|meth| report

CLI command

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

Rendered map

Line Spread

Demonstrates the `%%metro line_spread:` axis with one per-section override per section: `bundle` (default) merges shared lines onto one trunk that cascades downward, `centered` balances that bundle about the midline, and `rails` draws each line as a parallel rail with shared stations as interchanges.

Mermaid source

%%metro title: Line spread modes
%%metro style: dark
%%metro line: dna | DNA | #4CAF50
%%metro line: rna | RNA | #2196F3
%%metro line: cfdna | cfDNA | #E91E63

%%metro line_spread: bundle
%%metro line_spread: centered | centered_sec
%%metro line_spread: rails | rails_sec

%% Rail panel input/output files: the rails fan out from the CRAM terminus and
%% fan back in to the VCF terminus (a fan-in), each meeting a buffer-stop marker.
%% rna skips Filter, so Filter is a partial interchange: the rna rail bridges
%% straight over its connector rather than stopping there.
%%metro file: r_in | CRAM
%%metro file: r_out | VCF

%%metro grid: bundle_sec | 0,0
%%metro grid: centered_sec | 1,0
%%metro grid: rails_sec | 2,0

graph LR
    subgraph bundle_sec [bundle]
        b_in[Input]
        b_dna[DNA]
        b_rna[RNA]
        b_cf[cfDNA]
        b_out[QC]

        b_in -->|dna| b_dna
        b_in -->|rna| b_rna
        b_in -->|cfdna| b_cf
        b_dna -->|dna| b_out
        b_rna -->|rna| b_out
        b_cf -->|cfdna| b_out
    end

    subgraph centered_sec [centered]
        c_in[Align]
        c_dna[DNA]
        c_rna[RNA]
        c_cf[cfDNA]
        c_out[Merge]

        c_in -->|dna| c_dna
        c_in -->|rna| c_rna
        c_in -->|cfdna| c_cf
        c_dna -->|dna| c_out
        c_rna -->|rna| c_out
        c_cf -->|cfdna| c_out
    end

    subgraph rails_sec [rails]
        r_in[ ]
        r_call[Call]
        r_filter[Filter]
        r_annotate[Annotate]
        r_out[ ]

        r_in -->|dna,rna,cfdna| r_call
        r_call -->|dna,cfdna| r_filter
        r_call -->|rna| r_annotate
        r_filter -->|dna,cfdna| r_annotate
        r_annotate -->|dna,rna,cfdna| r_out
    end

    b_out -->|dna,rna,cfdna| c_in

CLI command

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

Rendered map

Cross Track Interchange

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

Marker Styles

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

%%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

Diagonal Labels

Opt-in diagonal station labels via `%%metro label_angle: 45`: a dense pre-processing trunk whose tilted names pack tighter than horizontal labels would, feeding a variant-calling section in the row below that fans out to three callers and back in -- the reserved vertical room keeps the hanging labels clear of the row beneath.

Mermaid source

%%metro title: Diagonal Labels (dense trunk)
%%metro style: dark
%%metro label_angle: 45
%%metro line: germline | Germline | #0570b0
%%metro line: tumor_only | Tumor only | #d62728
%%metro line: somatic | Tumor-normal pair | #756bb1
%%metro file: fastq_in | FASTQ
%%metro file: vcf_out | VCF
%%metro grid: preprocessing | 0,0
%%metro grid: variant_calling | 0,1

graph LR
    subgraph preprocessing [Pre-processing]
        %%metro exit: right | germline, tumor_only, somatic
        fastq_in[ ]
        fastqc[FastQC]
        fastp[FastP]
        umi[UMI consensus]
        bwa[BWA-MEM]
        merge_index[samtools merge/index]
        markdup[MarkDuplicates]
        bqsr[BaseRecalibrator]
        applybqsr[ApplyBQSR]
        mosdepth[mosdepth]
        ngscheckmate[NGSCheckmate]

        fastq_in -->|germline,tumor_only,somatic| fastqc
        fastqc -->|germline,tumor_only,somatic| fastp
        fastp -->|germline,tumor_only,somatic| umi
        umi -->|germline,tumor_only,somatic| bwa
        bwa -->|germline,tumor_only,somatic| merge_index
        merge_index -->|germline,tumor_only,somatic| markdup
        markdup -->|germline,tumor_only,somatic| bqsr
        bqsr -->|germline,tumor_only,somatic| applybqsr
        applybqsr -->|germline,tumor_only,somatic| mosdepth
        mosdepth -->|germline,tumor_only,somatic| ngscheckmate
    end

    subgraph variant_calling [Variant calling]
        %%metro entry: left | germline, tumor_only, somatic
        split[split by analysis]
        deepvariant[GATK]
        mutect[Mutect2]
        strelka[Strelka2]
        merge_vcf[merge VCFs]
        vcf_out[ ]

        split -->|germline| deepvariant
        split -->|tumor_only| mutect
        split -->|somatic| strelka
        deepvariant -->|germline| merge_vcf
        mutect -->|tumor_only| merge_vcf
        strelka -->|somatic| merge_vcf
        merge_vcf -->|germline,tumor_only,somatic| vcf_out
    end

    %% The dense angled-label trunk feeds the variant-calling section in the
    %% row below, which fans out to three callers (one per line) and fans
    %% back in at merge VCFs -- exercising the vertical room the hanging
    %% angled labels need above the row below.
    ngscheckmate -->|germline,tumor_only,somatic| split

CLI command

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

Rendered map

File Icons

Terminus icon variants: single-sheet `%%metro file:`, stacked `%%metro files:` for multiplicity, the `%%metro dir:` folder, and the optional `| banner` format strip.

Mermaid source

%%metro title: File Icon Variants (#532)
%%metro style: dark
%%metro line: main | Pipeline | #4CAF50

%%metro file: ref_in | FASTA | Reference
%%metro files: reads_in | FASTQ | Reads
%%metro files: aln_out | BAM | Alignments | banner
%%metro file: report_out | HTML/PDF | Report
%%metro dir: results_out | Results

graph LR
    subgraph inputs [Inputs]
        ref_in[ ]
        reads_in[ ]
        align[Align]
        ref_in -->|main| align
        reads_in -->|main| align
    end

    subgraph outputs [Outputs]
        %%metro entry: left | main
        collect[Collect]
        aln_out[ ]
        report_out[ ]
        results_out[ ]
        collect -->|main| aln_out
        collect -->|main| report_out
        collect -->|main| results_out
    end

    align -->|main| collect

CLI command

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

Rendered map

Legend Logo Placement

Demonstrates positioning the bundled legend+logo block: `%%metro legend: br | canvas` pins it to the empty lower-right canvas corner and `%%metro logo_scale:` enlarges the embedded logo. The directive also supports `| dx,dy` offsets and absolute `x,y` placement; the block auto-avoids sections and routes. The QC line shows a downward cross-column feeder dropping straight into its consumer section.

Mermaid source

%%metro title: Legend + logo placement
%%metro style: dark
%%metro logo: examples/placeholder_logo.png
%%metro logo_scale: 1.5
%%metro legend: br | canvas
%%metro file: fq_in | FASTQ
%%metro line: main | Main route | #3b82f6
%%metro line: qc | QC route | #e6842a
%%metro grid: input | 0,0
%%metro grid: trim | 1,0
%%metro grid: align | 2,0
%%metro grid: call | 3,0
%%metro grid: report | 4,0
%%metro grid: qc | 2,1
graph LR
    subgraph input [Input]
        %%metro exit: right | main
        %%metro exit: bottom | qc
        fq_in[ ]
        cat[Cat FASTQ]
        fq_in -->|main,qc| cat
    end
    subgraph trim [Trimming]
        %%metro entry: left | main
        %%metro exit: right | main
        trimg[Trim]
    end
    subgraph align [Alignment]
        %%metro entry: left | main
        %%metro exit: right | main
        bwa[BWA-MEM]
        sort[Sort]
        bwa -->|main| sort
    end
    subgraph call [Variant calling]
        %%metro entry: left | main
        %%metro exit: right | main
        caller[Caller]
    end
    subgraph report [Reporting]
        %%metro entry: left | main
        annot[Annotate]
        rep[Report]
        annot -->|main| rep
    end
    subgraph qc [Quality control]
        %%metro entry: left | qc
        fastqc[FastQC]
        multiqc[MultiQC]
        fastqc -->|qc| multiqc
    end
    cat -->|main| trimg
    trimg -->|main| bwa
    sort -->|main| caller
    caller -->|main| annot
    cat -->|qc| fastqc

CLI command

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

Rendered map

Legend Combo

Demonstrates `%%metro legend_combo:`: a normal (blue) and tumor (red) line travel together as a tumor-normal pair. The combo renders one legend row with a striped red+blue swatch. Normal travels only within the bundle so its individual row is suppressed, while tumor breaks away alone to Annotate and keeps its own row; the QC line is unaffected.

Mermaid source

%%metro title: Tumor-Normal Calling
%%metro style: dark
%%metro line: normal | Normal | #2196F3
%%metro line: tumor | Tumor | #E53935
%%metro line: qc | Quality Control | #4CAF50 | dashed
%%metro legend_combo: normal, tumor | Tumor-normal pair

graph LR
    fastq[FASTQ]
    align[Alignment]
    markdup[MarkDuplicates]
    bqsr[BQSR]
    fastqc[FastQC]
    call[Somatic Calling]
    annotate[Annotate]
    multiqc[MultiQC]

    fastq -->|normal,tumor| align
    align -->|normal,tumor| markdup
    markdup -->|normal,tumor| bqsr
    bqsr -->|normal,tumor| call
    call -->|tumor| annotate

    fastq -->|qc| fastqc
    fastqc -->|qc| multiqc

CLI command

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

Rendered map

Group Labels

Annotative `%%metro group:` band captions labelling sarek-style sub-families of callers (SNPs & Indels / SV & CNV / MSI) within a single section, without splitting them apart.

Mermaid source

%%metro title: Variant Calling with Group Bands
%%metro style: dark
%%metro line: caller | Variant Calling | #2db572

%%metro group: SNPs & Indels | freebayes, haplotypecaller, mutect2
%%metro group: SV & CNV | manta, cnvkit
%%metro group: MSI | msisensorpro

graph LR
    subgraph preprocess [Pre-processing]
        markdup[MarkDuplicates]
        recal[BaseRecalibrator]

        markdup -->|caller| recal
    end

    subgraph calling [Variant Calling]
        freebayes[FreeBayes]
        haplotypecaller[HaplotypeCaller]
        mutect2[Mutect2]
        manta[Manta]
        cnvkit[CNVkit]
        msisensorpro[MSIsensorpro]

        %% The callers sit in one horizontal row; the group bands beneath
        %% caption contiguous families along the x-axis (sarek-style).
        freebayes -->|caller| haplotypecaller
        haplotypecaller -->|caller| mutect2
        mutect2 -->|caller| manta
        manta -->|caller| cnvkit
        cnvkit -->|caller| msisensorpro
    end

    recal -->|caller| freebayes

CLI command

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

Rendered map

Off Track Outputs

Off-track file artefacts hung above a pre-processing trunk at the step that writes each one: `%%metro off_track:` on a producer-fed sink anchors it to its producer (not the section top), mirroring the off-track input mechanism for outputs. Each output gets its own column clear of the next station, and a step writing several files (MarkDup here) stacks them above it.

Mermaid source

%%metro title: Off-track outputs
%%metro line: main | Pre-processing | #3b82f6
%%metro off_track: bam_mapped, dedup_cram, recal_cram
%%metro file: bam_mapped | BAM
%%metro file: dedup_cram | CRAM
%%metro file: recal_cram | CRAM

graph LR
    subgraph preprocess [Pre-processing]
        fastq[FASTQ]
        bwa[BWA-MEM]
        convert[convert]
        markdup[MarkDup]
        bqsr[BQSR]
        ready[Ready]
        bam_mapped[ ]
        dedup_cram[ ]
        recal_cram[ ]

        fastq -->|main| bwa
        bwa -->|main| convert
        bwa -->|main| markdup
        convert -->|main| bqsr
        markdup -->|main| bqsr
        bqsr -->|main| ready

        bwa -->|main| bam_mapped
        markdup -->|main| dedup_cram
        bqsr -->|main| recal_cram
    end

CLI command

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

Rendered map

Tb File Termini

A `%%metro direction: TB` reporting section whose file outputs are line termini. Regression fixture: terminus file icons orient to a vertical flow, with the connector entering from the top.

Mermaid source

%%metro title: TB section file outputs
%%metro style: dark
%%metro directional: true
%%metro line: rna | RNA-seq | #1f9e89
%%metro line: dna | Variant | #2c7fb8
%%metro file: report_html | HTML | Report
%%metro file: bundle_zip | ZIP | Bundle
%%metro file: multiqc_html | HTML | MultiQC

graph LR
    subgraph analysis [Analysis]
        align[Align]
        call[Call]
        align -->|rna,dna| call
    end

    subgraph reporting [Reporting]
        %%metro direction: TB
        %%metro entry: left | rna, dna
        report[Build report]
        bundle[Zip bundle]
        multiqc[MultiQC]
        report_html[ ]
        bundle_zip[ ]
        multiqc_html[ ]

        report -->|rna,dna| report_html
        report -->|rna,dna| bundle
        bundle -->|rna,dna| bundle_zip
        report -->|rna,dna| multiqc
        multiqc -->|rna,dna| multiqc_html
    end

    call -->|rna,dna| report

CLI command

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

Rendered map

Disconnected Components

A connected three-section trunk plus a separate, wide disconnected section. Each weakly-connected component of the section graph is placed in its own local column grid and the components are stacked vertically, so the wide panel never inflates the trunk's columns or flings its later sections to the right.

Mermaid source

%%metro title: Disconnected Components
%%metro style: dark
%%metro line: main | Main Pipeline | #e63946
%%metro line: aux | Auxiliary Report | #0570b0

graph LR
    subgraph ingest [Ingest]
        in1[Read Input]
        in2[Validate]
        in1 -->|main| in2
    end

    subgraph process [Process]
        pr1[Align]
        pr2[Filter]
        pr1 -->|main| pr2
    end

    subgraph results [Results]
        re1[Summarise]
        re2[Publish]
        re1 -->|main| re2
    end

    subgraph wide_report [Standalone QC Report]
        w1[Collect]
        w2[Aggregate]
        w3[Annotate]
        w4[Normalise]
        w5[Visualise]
        w6[Export]
        w1 -->|aux| w2
        w2 -->|aux| w3
        w3 -->|aux| w4
        w4 -->|aux| w5
        w5 -->|aux| w6
    end

    in2 -->|main| pr1
    pr2 -->|main| re1

CLI command

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

Rendered map

Multi Section Cell

Multiple sections packed into one grid cell: a `%%metro grid:` directive names two comma-separated sections that share a cell and pack side-by-side along the flow axis. A short+long pair in one row aligns top-to-bottom with a long+short pair packed into the same column below it, freeing the bottom-left for the legend.

Mermaid source

%%metro title: Multi-section cell packing
%%metro line: main | Main | #4477aa | solid

%%metro grid: pre | 0,0
%%metro grid: short_a, long_a | 1,0
%%metro grid: norm | 2,0
%%metro grid: long_b, short_b | 1,1
%%metro grid: cons | 2,1

graph LR
    subgraph pre [Preprocessing]
        p1[Input] -->|main| p2[Trim]
    end
    subgraph short_a [GATK]
        a1[Call] -->|main| a2[Filter]
    end
    subgraph long_a [Variant Calling]
        b1[Pileup] -->|main| b2[Genotype]
        b2 -->|main| b3[Phase]
        b3 -->|main| b4[Recal]
        b4 -->|main| b5[Score]
        b5 -->|main| b6[Emit]
    end
    subgraph norm [Normalize]
        n1[Norm] -->|main| n2[Annotate]
    end
    subgraph long_b [Realignment]
        c1[Index] -->|main| c2[Realign]
        c2 -->|main| c3[Dedup]
        c3 -->|main| c4[BQSR]
        c4 -->|main| c5[Merge]
        c5 -->|main| c6[Sort]
    end
    subgraph short_b [Reporting]
        d1[Report] -->|main| d2[Summary]
    end
    subgraph cons [Consensus]
        e1[Consensus] -->|main| e2[Final]
    end
    p2 -->|main| a1
    a2 -->|main| b1
    b6 -->|main| n1
    p2 -->|main| c1
    c6 -->|main| d1
    d2 -->|main| e1

CLI command

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

Rendered map

Fanout Bundle Plus Spurs

A shared source fans out three ways at once: a same-column multi-line branch wrapping to the row below, plus single-line spurs peeling off the same junction. The branch bundle keeps its concentric fan order, each spur's descent fuses onto the bundle rather than crossing it, and the single-line spur sections ride their own trunks.

Mermaid source

%%metro title: Fan-out bundle plus spurs
%%metro line: a | Line A | #e6007e
%%metro line: b | Line B | #2db572
%%metro line: c | Line C | #2b6cb0
%%metro grid: trunk | 0,0
%%metro grid: branch | 0,1
%%metro grid: solo_a | 1,0
%%metro grid: solo_b | 1,1

graph LR
    subgraph trunk [Trunk]
        %%metro exit: right | a, b, c
        x1[X1]
        x2[X2]
        x1 -->|a,b,c| x2
    end

    subgraph branch [Branch]
        %%metro entry: left | a, b, c
        y1[Y1]
        y2[Y2]
        y1 -->|a,b,c| y2
    end

    subgraph solo_a [SoloA]
        %%metro entry: left | a
        z1[Z1]
        z2[Z2]
        z1 -->|a| z2
    end

    subgraph solo_b [SoloB]
        %%metro entry: left | b
        w1[W1]
        w2[W2]
        w1 -->|b| w2
    end

    x2 -->|a,b,c| y1
    x2 -->|a| z1
    x2 -->|b| w1

CLI command

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

Rendered map

Folded Corridor Distinct Lanes

Two distinct lines share a folded RL return corridor: they co-travel the trunk and fold drop as adjacent lanes, diverge where one line bypasses a section while the other routes through it, and reconverge at the final section. Every shared channel keeps the two lines an OFFSET_STEP apart rather than collapsing one stroke onto the other.

Mermaid source

%%metro title: Folded Corridor Distinct Lanes
%%metro style: dark
%%metro line: dna | DNA | #4a90d9
%%metro line: rna | RNA | #e63946
%%metro grid: preprocessing | 0,0
%%metro grid: gatk | 1,0
%%metro grid: variant_calling | 2,0
%%metro grid: normalization | 2,1
%%metro grid: consensus | 1,1
%%metro grid: realignment | 0,1

graph LR
    subgraph preprocessing [Pre-processing]
        %%metro exit: right | dna, rna
        pp1[Trim]
        pp2[Align]
        pp1 -->|dna,rna| pp2
    end
    subgraph gatk [GATK]
        %%metro entry: left | dna, rna
        %%metro exit: right | dna, rna
        gk1[BQSR]
        gk2[Apply]
        gk1 -->|dna,rna| gk2
    end
    subgraph variant_calling [Variant Calling]
        %%metro entry: left | dna, rna
        %%metro exit: bottom | dna, rna
        vc1[Call]
        vc2[Filter]
        vc1 -->|dna,rna| vc2
    end
    subgraph normalization [Normalization]
        %%metro direction: RL
        %%metro entry: top | dna, rna
        %%metro exit: left | dna, rna
        nz1[Decompose]
        nz2[Norm]
        nz1 -->|dna,rna| nz2
    end
    subgraph consensus [Consensus]
        %%metro direction: RL
        %%metro entry: right | dna
        %%metro exit: left | dna
        cs1[Merge]
        cs2[Vote]
        cs1 -->|dna| cs2
    end
    subgraph realignment [Realignment]
        %%metro direction: RL
        %%metro entry: right | dna, rna
        rl1[Realign]
        rl2[Recall]
        rl1 -->|dna,rna| rl2
    end
    pp2 -->|dna,rna| gk1
    gk2 -->|dna,rna| vc1
    vc2 -->|dna,rna| nz1
    nz2 -->|dna| cs1
    nz2 -->|rna| rl1
    cs2 -->|dna| rl1

CLI command

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

Rendered map

Realistic Pipelines

Genomic Pipeline

Multi-section genomic variant-calling pipeline: same-direction sections stacked in one column (serpentine carriage-return) plus a multi-row QC collector fan-in descending a shared inter-column corridor.

Mermaid source

%%metro title: Variant Calling Pipeline
%%metro style: dark
%%metro legend: br
%%metro line_order: definition
%%metro center_ports: true
%%metro compact_offsets: true
%%metro file: fastq_in | FASTQ
%%metro file: bam_in | BAM
%%metro file: cram_in | CRAM
%%metro file: vcf_out | VCF
%%metro file: report_out | HTML
%%metro line: germline | Germline | #0570b0
%%metro line: tumor_only | Tumor only | #d62728
%%metro line: somatic | Tumor-normal pair | #756bb1

graph LR
    subgraph preprocessing [Pre-processing]
        %%metro exit: right | germline, tumor_only, somatic
        fastq_in[ ]
        bam_in[ ]
        fastqc[FastQC]
        fastp[FastP]
        umi[UMI consensus]
        bwa[BWA-MEM]
        bwa2[BWA-MEM2]
        dragmap[DragMap]
        sentieon_bwa[Sentieon BWA]
        merge_index[samtools merge/index]
        markdup[MarkDuplicates]
        sentieon_dedup[Sentieon Dedup]
        bqsr[BaseRecalibrator]
        applybqsr[ApplyBQSR]
        mosdepth[mosdepth]
        ngscheckmate[NGSCheckmate]

        fastq_in -->|germline,tumor_only,somatic| fastqc
        fastq_in -->|germline,tumor_only,somatic| fastp
        bam_in -->|germline,tumor_only,somatic| fastp
        fastp -->|germline,tumor_only,somatic| umi
        umi -->|germline,tumor_only,somatic| bwa
        umi -->|germline,tumor_only,somatic| bwa2
        umi -->|germline,tumor_only,somatic| dragmap
        umi -->|germline,tumor_only,somatic| sentieon_bwa
        bwa -->|germline,tumor_only,somatic| merge_index
        bwa2 -->|germline,tumor_only,somatic| merge_index
        dragmap -->|germline,tumor_only,somatic| merge_index
        sentieon_bwa -->|germline,tumor_only,somatic| merge_index
        merge_index -->|germline,tumor_only,somatic| markdup
        merge_index -->|germline,tumor_only,somatic| sentieon_dedup
        markdup -->|germline,tumor_only,somatic| bqsr
        sentieon_dedup -->|germline,tumor_only,somatic| bqsr
        bqsr -->|germline,tumor_only,somatic| applybqsr
        applybqsr -->|germline,tumor_only,somatic| mosdepth
        applybqsr -->|germline,tumor_only,somatic| ngscheckmate
    end

    subgraph variant_calling [Variant calling]
        %%metro entry: left | germline, tumor_only, somatic
        %%metro exit: right | germline, tumor_only, somatic
        cram_in[ ]
        haplotypecaller[HaplotypeCaller]
        deepvariant[DeepVariant]
        sentieon_dnascope[Sentieon DNAscope]
        sentieon_haplotyper[Sentieon Haplotyper]
        freebayes[FreeBayes]
        strelka[Strelka]
        mpileup[bcftools mpileup]
        mutect2[Mutect2]
        lofreq[LoFreq]
        muse[MuSE]
        sentieon_tnscope[Sentieon TNscope]
        manta[Manta]
        tiddit[TIDDIT]
        ascat[ASCAT]
        cnvkit[CNVkit]
        controlfreec[Control-FREEC]
        indexcov[indexcov]
        msisensor2[MSIsensor2]
        msisensorpro[MSIsensor-pro]
        vcfs[ ]

        cram_in -->|germline| haplotypecaller
        cram_in -->|germline| deepvariant
        cram_in -->|germline| sentieon_dnascope
        cram_in -->|germline| sentieon_haplotyper
        cram_in -->|germline,tumor_only,somatic| freebayes
        cram_in -->|germline,somatic| strelka
        cram_in -->|germline,tumor_only,somatic| mpileup
        cram_in -->|tumor_only,somatic| mutect2
        cram_in -->|tumor_only| lofreq
        cram_in -->|somatic| muse
        cram_in -->|tumor_only,somatic| sentieon_tnscope
        cram_in -->|germline,tumor_only,somatic| manta
        cram_in -->|germline,tumor_only,somatic| tiddit
        cram_in -->|somatic| ascat
        cram_in -->|germline,tumor_only,somatic| cnvkit
        cram_in -->|tumor_only,somatic| controlfreec
        cram_in -->|germline,somatic| indexcov
        cram_in -->|tumor_only| msisensor2
        cram_in -->|somatic| msisensorpro

        haplotypecaller -->|germline| vcfs
        deepvariant -->|germline| vcfs
        sentieon_dnascope -->|germline| vcfs
        sentieon_haplotyper -->|germline| vcfs
        freebayes -->|germline,tumor_only,somatic| vcfs
        strelka -->|germline,somatic| vcfs
        mpileup -->|germline,tumor_only,somatic| vcfs
        mutect2 -->|tumor_only,somatic| vcfs
        lofreq -->|tumor_only| vcfs
        muse -->|somatic| vcfs
        sentieon_tnscope -->|tumor_only,somatic| vcfs
        manta -->|germline,tumor_only,somatic| vcfs
        tiddit -->|germline,tumor_only,somatic| vcfs
        ascat -->|somatic| vcfs
        cnvkit -->|germline,tumor_only,somatic| vcfs
        controlfreec -->|tumor_only,somatic| vcfs
        indexcov -->|germline,somatic| vcfs
        msisensor2 -->|tumor_only| vcfs
        msisensorpro -->|somatic| vcfs
    end

    subgraph post_vc [Post-processing]
        filter_vcfs[Filter VCFs]
        normalize[Normalize]
        concatenate[Concatenate]
        consensus[Consensus]
        varlociraptor[Varlociraptor]
        bcftools_stats[bcftools stats]
        vcftools[VCFtools]

        filter_vcfs -->|germline,tumor_only,somatic| normalize
        normalize -->|germline,tumor_only,somatic| concatenate
        concatenate -->|germline,tumor_only,somatic| consensus
        consensus -->|germline,tumor_only,somatic| varlociraptor
        varlociraptor -->|germline,tumor_only,somatic| bcftools_stats
        bcftools_stats -->|germline,tumor_only,somatic| vcftools
    end

    subgraph annotation [Annotation]
        snpeff[snpEff]
        vep[VEP]
        bcftools_ann[bcftools annotate]
        snpsift[SnpSift]

        snpeff -->|germline,tumor_only,somatic| vep
        vep -->|germline,tumor_only,somatic| bcftools_ann
        bcftools_ann -->|germline,tumor_only,somatic| snpsift
    end

    subgraph reporting [Reporting]
        multiqc[MultiQC]
        vcf_out[ ]
        report_out[ ]

        multiqc -->|germline,tumor_only,somatic| report_out
        snpsift_to_vcf[ ]
        snpsift_to_vcf -->|germline,tumor_only,somatic| vcf_out
    end

    %% Inter-section edges
    applybqsr -->|germline,tumor_only,somatic| cram_in
    vcfs -->|germline,tumor_only,somatic| filter_vcfs
    vcftools -->|germline,tumor_only,somatic| snpeff
    snpsift -->|germline,tumor_only,somatic| snpsift_to_vcf
    fastqc -->|germline,tumor_only,somatic| multiqc
    mosdepth -->|germline,tumor_only,somatic| multiqc
    bcftools_stats -->|germline,tumor_only,somatic| multiqc

CLI command

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

Rendered map

Longread Variant Calling

Dense long-read variant-calling pipeline (six lines, nine sections): exercises inter-section routing around non-connecting section boxes, cross-row feeds via the inter-row gap, same-line bundle coincidence, and a same-colour crossover bridge.

Mermaid source

%%metro title: Long-read Variant Calling
%%metro style: dark
%%metro directional: true
%%metro files: fastq_in | FASTQ
%%metro files: bam_in | BAM
%%metro files: ubam_in | uBAM
%%metro line: ubam | uBAM | #0570b0
%%metro line: fastq | FASTQ | #2db572
%%metro line: bam | BAM | #f5c542
%%metro line: other | Other | #ff8c00
%%metro line: snvvcf | SNV VCF | #e63946
%%metro line: svvcf | SV VCF | #9d4edd
%%metro legend: tl

graph LR
    subgraph preprocessing [Pre-processing]

        fastq_in[ ]
        bam_in[ ]
        ubam_in[ ]
        cat_fastq[cat FASTQ]
        samtools_merge[samtools\nmerge]
        minimap2_align[minimap2]
        samtools_sort_index[samtools\nsort/index]
        mosdepth[mosdepth]

        fastq_in -->|fastq| cat_fastq
        ubam_in -->|ubam| samtools_merge
        bam_in -->|bam| samtools_merge
        cat_fastq -->|fastq| minimap2_align
        samtools_merge -->|ubam| minimap2_align
        minimap2_align -->|bam| samtools_sort_index
        samtools_merge -->|bam| samtools_sort_index
        samtools_sort_index -->|bam| mosdepth
    end

    subgraph small_variants [Small variant calling]

        clair3[Clair3]
        deepvariant[Deepvariant]
    end

    subgraph cnv_calling [CNVs]

        ontspectre_cnvcaller[ont-spectre CNVCaller]
    end

    subgraph tr_calling [Repeats]

        longtr[LongTR]
        straglr[Straglr]
        trgt[TRGT]
    end

    subgraph phasing [Phasing]

        whatshap_phase[WhatsHap Phase]
        whatshap_haplotag[WhatsHap Haplotag]

        whatshap_phase -->|bam,snvvcf| whatshap_haplotag
    end

    subgraph structural_variants [Structural Variants]

        sniffles[Sniffles]
        cutesv[CuteSV]
        jasminesv_callers[Jasmine merge callers]

        sniffles -->|svvcf,bam| jasminesv_callers
        cutesv -->|svvcf,bam| jasminesv_callers
    end

    subgraph jointcalling [Joint Calling]

        jasminesv_samples[Jasmine merge samples]
        glnexus[GLNexus]
    end

    subgraph annotation [Annotation]

        vep[VEP]
        snpeff[SnpEff]
        annotsv[AnnotSV]
    end

    subgraph reports [Reports]

        geneyx[Geneyx]
        sv_report[SV Report]
    end


    %% Inter-section edges
    samtools_sort_index -->|bam| clair3
    samtools_sort_index -->|bam| deepvariant
    samtools_sort_index -->|bam| longtr
    samtools_sort_index -->|bam| straglr
    samtools_sort_index -->|bam| trgt

    mosdepth -->|other| ontspectre_cnvcaller

    straglr -->|other| geneyx

    clair3 -->|snvvcf| ontspectre_cnvcaller
    deepvariant -->|snvvcf| ontspectre_cnvcaller

    clair3 -->|bam,snvvcf| whatshap_phase
    deepvariant -->|bam,snvvcf| whatshap_phase

    clair3 -->|snvvcf| glnexus
    deepvariant -->|snvvcf| glnexus

    clair3 -->|snvvcf| vep
    deepvariant -->|snvvcf| vep

    whatshap_haplotag -->|bam| sniffles
    whatshap_haplotag -->|bam| cutesv
    whatshap_haplotag -->|bam| jasminesv_samples

    ontspectre_cnvcaller -->|other| geneyx

    sniffles -->|svvcf| jasminesv_samples
    sniffles -->|svvcf| vep
    sniffles -->|svvcf| snpeff
    sniffles -->|svvcf| annotsv
    sniffles -->|svvcf| geneyx

    cutesv -->|svvcf| jasminesv_samples
    cutesv -->|svvcf| vep
    cutesv -->|svvcf| snpeff
    cutesv -->|svvcf| annotsv
    cutesv -->|svvcf| geneyx

    jasminesv_callers -->|svvcf| jasminesv_samples
    jasminesv_callers -->|svvcf| vep
    jasminesv_callers -->|svvcf| snpeff
    jasminesv_callers -->|svvcf| annotsv
    jasminesv_callers -->|svvcf| geneyx
    jasminesv_callers -->|svvcf| sv_report

    snpeff -->|svvcf| sv_report
    annotsv -->|svvcf| sv_report

    glnexus -->|snvvcf| vep

CLI command

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

Rendered map

Sarek Metro

Integration showcase: a sarek-style variant-calling pipeline drawn with diagonal (45-degree) labels for tight column packing, an off-track FASTQ input, file termini, marker styles, and a `%%metro line_spread: rails` panel where each caller keeps its own rail and shared stations render as interchanges.

Mermaid source

%%metro title: Example analysis pathways
%%metro caption: Adapted from: Fellows Yates, James A., et al. PeerJ 9 (2021)
%%metro style: dark
%%metro logo: examples/nf-core-sarek_logo_light.png | examples/nf-core-sarek_logo_dark.png
%%metro logo_scale: 1.0
%%metro font_scale: 1.3
%%metro legend_logo_gap: 40
%%metro legend: br
%%metro label_angle: 45
%%metro line_spread: rails | calling
%%metro grid: preprocessing | 0,0
%%metro grid: variantcalling | 1,0
%%metro grid: annotation | 2,0
%%metro grid: calling | 0,1,1,3

%%metro line: core | Core workflow | #2db572
%%metro line: germline | Germline | #0570b0
%%metro line: tumor_only | Tumor only | #d62728
%%metro line: pair_n | Tumor-normal (normal) | #0570b0
%%metro line: pair_t | Tumor-normal (tumor) | #d62728

%% Tumor-normal pair is the normal + tumor lines bundled together; give the
%% combination a single legend entry instead of two separate rows.
%%metro legend_combo: pair_n, pair_t | Tumor-normal pair

%%metro files: ubam_in | uBAM
%%metro files: spring_in | spring
%%metro files: fastq_in | FASTQ
%%metro file: vcf_ann | VCF
%%metro file: vcf_vc | VCF
%%metro files: cram_call | CRAM
%%metro file: out | VCF
%%metro file: out | TXT
%%metro files: out | ...

%% Intermediate alignment artefacts written off the trunk at the step that
%% produces them (mapping, samtools, recalibration prep, applybqsr).
%%metro files: mapped_out | BAM/CRAM
%%metro files: samtools_out | CRAM
%%metro files: recalprep_out | CRAM
%%metro files: recal_out | CRAM

%% ubam and spring need conversion, so they feed convert; fastq is already in
%% the right format and joins the trunk at FastQC, past convert.  spring and
%% fastq lift off the trunk as off-track inputs with an S-curve.  The bam/cram
%% outputs hang off their producer the same way (off_track anchors a sink to
%% its source).
%%metro off_track: fastq_in
%%metro off_track: spring_in
%%metro off_track: mapped_out
%%metro off_track: samtools_out
%%metro off_track: recalprep_out
%%metro off_track: recal_out
%%metro off_track: vcf_vc

%% Marker key. Optional steps use the standard station pill (undistinguished);
%% only mandatory / accelerated steps get a marker shape. Acceleration is shown
%% by fill colour: Parabricks (green), Sentieon (navy), or both (teal) on
%% whatever shape the step already carries.
%%metro marker_legend: square, solid | Mandatory
%%metro marker_legend: square, #4CAF50 | Parabricks accelerated
%%metro marker_legend: square, #1b3a6b | Sentieon accelerated
%%metro marker_legend: square, #2f7f74 | Parabricks & Sentieon accelerated
%%metro marker_legend: pill, open | Expanded in pathways panel

%% Caller families along the pathways trunk.
%%metro group: SNPs & Indels | deepvariant, freebayes, haplotypecaller, haplotyper, dnascope, tnscope, lofreq, muse, mpileup, mutect2, strelka2
%%metro group: SV & CNV | indexcov, manta, tiddit, ascat, controlfreec, cnvkit
%%metro group: MSI | msisensor2, msisensorpro

%% --- markers: mandatory steps get a square; acceleration is the fill colour.
%% mapping and markduplicates are accelerable by both Parabricks and Sentieon
%% (teal); the BQSR steps are Parabricks-only (green); the Sentieon callers in
%% the pathways panel are Sentieon-only (navy).
%%metro marker: convert | square, solid
%%metro marker: bam_convert | square, solid
%%metro marker: mapping | square, #2f7f74
%%metro marker: markduplicates | square, #2f7f74
%%metro marker: prepare_recal | circle, #4CAF50
%%metro marker: applybqsr | circle, #4CAF50
%%metro marker: vc_anchor | pill, open

%% Sentieon-accelerated callers in the pathways panel (navy circles).  Single-rail
%% callers (haplotyper, dnascope) show the marker; tnscope spans two rails and
%% renders as a plain interchange (a marker on a spanning rail station is drawn
%% as the interchange bar, not the glyph).
%%metro marker: haplotyper | circle, #1b3a6b
%%metro marker: dnascope | circle, #1b3a6b
%%metro marker: tnscope | circle, #1b3a6b


graph LR
    subgraph preprocessing [Pre-processing]
        ubam_in[ ]
        spring_in[ ]
        fastq_in[ ]
        convert[convert]
        fastqc[FastQC]
        umi[UMI]
        fastp[FastP]
        bbsplit[BBsplit]
        mapping[mapping]
        bam_convert[convert]
        markduplicates[markduplicates]
        mosdepth[mosdepth, samtools]
        prepare_recal[prepare recalibration]
        applybqsr[applybqsr]
        mosdepth_qc[mosdepth, samtools]
        ngscheckmate[NGSCheckmate]
        mapped_out[ ]
        samtools_out[ ]
        recalprep_out[ ]
        recal_out[ ]

        ubam_in -->|core| convert
        spring_in -->|core| convert
        fastq_in -->|core| fastqc
        convert -->|core| fastqc
        fastqc -->|core| umi
        umi -->|core| fastp
        fastp -->|core| bbsplit
        bbsplit -->|core| mapping
        mapping -->|core| bam_convert
        mapping -->|core| markduplicates
        bam_convert -->|core| mosdepth
        markduplicates -->|core| mosdepth
        mosdepth -->|core| prepare_recal
        prepare_recal -->|core| applybqsr
        applybqsr -->|core| mosdepth_qc
        mosdepth_qc -->|core| ngscheckmate

        mapping -->|core| mapped_out
        mosdepth -->|core| samtools_out
        prepare_recal -->|core| recalprep_out
        applybqsr -->|core| recal_out
    end

    subgraph variantcalling [Variant calling]
        vc_anchor[variant calling]
        bcftools[bcftools]
        samtools_vc[samtools]
        varlociraptor[Varlociraptor]
        finalise[finalise]
        normalise[normalise]
        consensus[consensus]
        _vc_merge[ ]
        vcf_vc[ ]

        vc_anchor -->|core| bcftools
        bcftools -->|core| samtools_vc
        samtools_vc -->|core| varlociraptor
        samtools_vc -->|core| finalise
        finalise -->|core| normalise
        normalise -->|core| consensus
        varlociraptor -->|core| _vc_merge
        consensus -->|core| _vc_merge
        _vc_merge -->|core| vcf_vc
    end

    subgraph annotation [Annotation]
        snpeff[snpEff]
        ensemblvep[ensemblVEP]
        bcftools_annotate[bcftools annotate]
        multiqc[MultiQC]
        vcf_ann[ ]

        snpeff -->|core| ensemblvep
        ensemblvep -->|core| bcftools_annotate
        bcftools_annotate -->|core| multiqc
        multiqc -->|core| vcf_ann
    end

    subgraph calling [Example analysis pathways]
        cram_call[ ]
        deepvariant[DeepVariant]
        freebayes[FreeBayes]
        haplotypecaller[HaplotypeCaller]
        haplotyper[Sentieon Haplotyper]
        dnascope[Sentieon DNAscope]
        tnscope[Sentieon TNscope]
        lofreq[LoFreq]
        muse[MuSE]
        mpileup[mpileup]
        mutect2[Mutect2]
        strelka2[Strelka2]
        indexcov[indexcov]
        manta[Manta]
        tiddit[TIDDIT]
        ascat[ASCAT]
        controlfreec[Control-FREEC]
        cnvkit[CNVkit]
        msisensor2[MSIsensor2]
        msisensorpro[MSIsensor-pro]
        out[ ]

        %% Germline route (top rail): deepvariant, haplotypecaller, haplotyper,
        %% dnascope are germline-only; freebayes/mpileup/strelka2/manta/tiddit/
        %% cnvkit/indexcov are shared.
        cram_call -->|germline| deepvariant
        deepvariant -->|germline| freebayes
        freebayes -->|germline| haplotypecaller
        haplotypecaller -->|germline| haplotyper
        haplotyper -->|germline| dnascope
        dnascope -->|germline| mpileup
        mpileup -->|germline| strelka2
        strelka2 -->|germline| indexcov
        indexcov -->|germline| manta
        manta -->|germline| tiddit
        tiddit -->|germline| cnvkit
        cnvkit -->|germline| out

        %% Tumour-only route (middle rail): tnscope, lofreq, mutect2, msisensor2
        %% join here; mpileup/indexcov run tumour but not the combined pair.
        cram_call -->|tumor_only| freebayes
        freebayes -->|tumor_only| tnscope
        tnscope -->|tumor_only| lofreq
        lofreq -->|tumor_only| mpileup
        mpileup -->|tumor_only| mutect2
        mutect2 -->|tumor_only| indexcov
        indexcov -->|tumor_only| manta
        manta -->|tumor_only| tiddit
        tiddit -->|tumor_only| controlfreec
        controlfreec -->|tumor_only| cnvkit
        cnvkit -->|tumor_only| msisensor2
        msisensor2 -->|tumor_only| out

        %% Tumour-normal pair route (bottom rail): muse, ascat, msisensorpro are
        %% combined-only; strelka2 runs germline + combined (not tumour-only).
        cram_call -->|pair_n,pair_t| freebayes
        freebayes -->|pair_n,pair_t| tnscope
        tnscope -->|pair_n,pair_t| muse
        muse -->|pair_n,pair_t| mutect2
        mutect2 -->|pair_n,pair_t| strelka2
        strelka2 -->|pair_n,pair_t| manta
        manta -->|pair_n,pair_t| tiddit
        tiddit -->|pair_n,pair_t| ascat
        ascat -->|pair_n,pair_t| controlfreec
        controlfreec -->|pair_n,pair_t| cnvkit
        cnvkit -->|pair_n,pair_t| msisensorpro
        msisensorpro -->|pair_n,pair_t| out
    end

    %% Inter-section: core workflow flows through the top three sections.
    ngscheckmate -->|core| vc_anchor
    _vc_merge -->|core| snpeff

CLI command

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

Rendered map

Differentialabundance

nf-core/differentialabundance with four input lines, off-track gene-set inputs, and a bypass-heavy reporting row. Uses `%%metro center_ports: true`.

Mermaid source

%%metro title: nf-core/differentialabundance
%%metro logo: examples/nf-core-differentialabundance_logo_light.png | examples/nf-core-differentialabundance_logo_dark.png
%%metro style: dark
%%metro legend: bl
%%metro line_order: definition
%%metro center_ports: true
%%metro compact_offsets: true
%%metro file: meta_in | YAML | Contrasts
%%metro file: meta_in | CSV | Samples
%%metro file: matrix_in | TSV | Matrix
%%metro file: cel_in | CEL | Affy CEL
%%metro file: mq_in | TSV | MaxQuant
%%metro file: geo_in | STR | GEO ID
%%metro file: gtf_in | GTF | GTF
%%metro file: gmt_in | GMT | Gene sets
%%metro file: net_in | TSV | Network
%%metro file: report_html | HTML | Report
%%metro file: bundle_zip | ZIP | Bundle
%%metro file: shiny_html | HTML | Shiny
%%metro file: plots_png | PNG | Plots
%%metro line: rnaseq | RNA-seq counts | #2db572
%%metro line: affy | Affymetrix microarray | #e6550d
%%metro line: maxquant | MaxQuant proteomics | #0570b0
%%metro line: geo | GEO SOFT file | #756bb1
%%metro grid: data_prep | 0,0,2,1
%%metro grid: differential | 1,0,1,1
%%metro grid: functional | 2,0,1,1
%%metro grid: reporting | 3,0,1,1
%%metro grid: plots | 2,1,1,1
%%metro off_track: gmt_in, net_in

graph LR
    subgraph data_prep [Data import and preparation]
        %%metro exit: right | rnaseq, affy, maxquant, geo
        meta_in[ ]
        matrix_in[ ]
        gtf_in[ ]
        cel_in[ ]
        mq_in[ ]
        geo_in[ ]
        gtf_to_table[GTF to table]
        affy_load[affy load]
        proteus[proteus]
        geoquery[GEOquery]
        validator[Validate]
        matrix_filter[Filter matrix]

        meta_in -->|rnaseq,affy,maxquant,geo| validator
        matrix_in -->|rnaseq| validator
        gtf_in -->|rnaseq,maxquant| gtf_to_table
        gtf_to_table -->|rnaseq,maxquant| validator
        cel_in -->|affy| affy_load
        affy_load -->|affy| validator
        mq_in -->|maxquant| proteus
        proteus -->|maxquant| validator
        geo_in -->|geo| geoquery
        geoquery -->|geo| validator
        validator -->|rnaseq,affy,maxquant,geo| matrix_filter
    end

    subgraph differential [Differential analysis]
        %%metro entry: left | rnaseq, affy, maxquant, geo
        %%metro exit: right | rnaseq, affy, maxquant, geo
        limma[limma]
        deseq2[DESeq2]
        dream[dream]
        propd[propd]
        annotate[Annotate results]

        limma -->|rnaseq,affy| annotate
        deseq2 -->|rnaseq| annotate
        dream -->|rnaseq| annotate
        propd -->|rnaseq| annotate
    end

    subgraph functional [Functional enrichment]
        %%metro entry: left | rnaseq, affy, maxquant, geo
        %%metro exit: right | rnaseq, affy, maxquant, geo
        gmt_in[ ]
        net_in[ ]
        gsea[GSEA]
        gprofiler2[gprofiler2]
        decoupler[decoupler]
        grea[grea]

        gmt_in -->|rnaseq,affy,maxquant,geo| gsea
        net_in -->|rnaseq,affy,maxquant,geo| decoupler
    end

    subgraph reporting [Reporting]
        %%metro entry: left | rnaseq, affy, maxquant, geo
        shinyngs[shinyngs]
        quarto[Quarto report]
        bundle[Zip bundle]
        shiny_html[ ]
        report_html[ ]
        bundle_zip[ ]

        shinyngs -->|rnaseq,affy,maxquant,geo| shiny_html
        quarto -->|rnaseq,affy,maxquant,geo| report_html
        quarto -->|rnaseq,affy,maxquant,geo| bundle
        bundle -->|rnaseq,affy,maxquant,geo| bundle_zip
    end

    subgraph plots [Plots]
        %%metro entry: left | rnaseq, affy, maxquant, geo
        plot_expl[Exploratory]
        plot_diff[Differential]
        plots_png[ ]

        plot_expl -->|rnaseq,affy,maxquant,geo| plots_png
        plot_diff -->|rnaseq,affy,maxquant,geo| plots_png
    end

    %% Inter-section edges
    matrix_filter -->|rnaseq,affy,maxquant,geo| limma
    matrix_filter -->|rnaseq| deseq2
    matrix_filter -->|rnaseq| dream
    matrix_filter -->|rnaseq| propd
    %% Section 2 -> Section 3 (functional from differential results)
    limma -->|rnaseq,affy,maxquant,geo| gsea
    limma -->|rnaseq,affy,maxquant,geo| gprofiler2
    limma -->|rnaseq,affy,maxquant,geo| decoupler
    limma -->|rnaseq| grea
    %% Section 2 -> Section 4 (plots are parallel, both from differential trunk)
    limma -->|rnaseq,affy,maxquant,geo| plot_expl
    limma -->|rnaseq,affy,maxquant,geo| plot_diff
    %% Section 2/3 -> Section 5 (reporting from differential + functional)
    limma -->|rnaseq,affy,maxquant,geo| shinyngs
    limma -->|rnaseq,affy,maxquant,geo| quarto
    gsea -->|rnaseq,affy,maxquant,geo| quarto
    gprofiler2 -->|rnaseq,affy,maxquant,geo| quarto
    decoupler -->|rnaseq,affy,maxquant,geo| quarto
    grea -->|rnaseq| quarto

CLI command

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

Rendered map

Differentialabundance Default

Same nf-core/differentialabundance map at default (uncentered) layout — useful for spotting regressions that only show with default port placement.

Mermaid source

%%metro title: nf-core/differentialabundance
%%metro logo: examples/nf-core-differentialabundance_logo_light.png | examples/nf-core-differentialabundance_logo_dark.png
%%metro style: dark
%%metro legend: bl
%%metro line_order: definition
%%metro compact_offsets: true
%%metro file: meta_in | YAML | Contrasts
%%metro file: meta_in | CSV | Samples
%%metro file: matrix_in | TSV | Matrix
%%metro file: cel_in | CEL | Affy CEL
%%metro file: mq_in | TSV | MaxQuant
%%metro file: geo_in | STR | GEO ID
%%metro file: gtf_in | GTF | GTF
%%metro file: gmt_in | GMT | Gene sets
%%metro file: net_in | TSV | Network
%%metro file: report_html | HTML | Report
%%metro file: bundle_zip | ZIP | Bundle
%%metro file: shiny_html | HTML | Shiny
%%metro file: plots_png | PNG | Plots
%%metro line: rnaseq | RNA-seq counts | #2db572
%%metro line: affy | Affymetrix microarray | #e6550d
%%metro line: maxquant | MaxQuant proteomics | #0570b0
%%metro line: geo | GEO SOFT file | #756bb1
%%metro grid: data_prep | 0,0,2,1
%%metro grid: differential | 1,0,1,1
%%metro grid: functional | 2,0,1,1
%%metro grid: reporting | 3,0,1,1
%%metro grid: plots | 2,1,1,1
%%metro off_track: gmt_in, net_in

graph LR
    subgraph data_prep [Data import and preparation]
        %%metro exit: right | rnaseq, affy, maxquant, geo
        meta_in[ ]
        matrix_in[ ]
        gtf_in[ ]
        cel_in[ ]
        mq_in[ ]
        geo_in[ ]
        gtf_to_table[GTF to table]
        affy_load[affy load]
        proteus[proteus]
        geoquery[GEOquery]
        validator[Validate]
        matrix_filter[Filter matrix]

        meta_in -->|rnaseq,affy,maxquant,geo| validator
        matrix_in -->|rnaseq| validator
        gtf_in -->|rnaseq,maxquant| gtf_to_table
        gtf_to_table -->|rnaseq,maxquant| validator
        cel_in -->|affy| affy_load
        affy_load -->|affy| validator
        mq_in -->|maxquant| proteus
        proteus -->|maxquant| validator
        geo_in -->|geo| geoquery
        geoquery -->|geo| validator
        validator -->|rnaseq,affy,maxquant,geo| matrix_filter
    end

    subgraph differential [Differential analysis]
        %%metro entry: left | rnaseq, affy, maxquant, geo
        %%metro exit: right | rnaseq, affy, maxquant, geo
        limma[limma]
        deseq2[DESeq2]
        dream[dream]
        propd[propd]
        annotate[Annotate results]

        limma -->|rnaseq,affy| annotate
        deseq2 -->|rnaseq| annotate
        dream -->|rnaseq| annotate
        propd -->|rnaseq| annotate
    end

    subgraph functional [Functional enrichment]
        %%metro entry: left | rnaseq, affy, maxquant, geo
        %%metro exit: right | rnaseq, affy, maxquant, geo
        gmt_in[ ]
        net_in[ ]
        gsea[GSEA]
        gprofiler2[gprofiler2]
        decoupler[decoupler]
        grea[grea]

        gmt_in -->|rnaseq,affy,maxquant,geo| gsea
        net_in -->|rnaseq,affy,maxquant,geo| decoupler
    end

    subgraph reporting [Reporting]
        %%metro entry: left | rnaseq, affy, maxquant, geo
        shinyngs[shinyngs]
        quarto[Quarto report]
        bundle[Zip bundle]
        shiny_html[ ]
        report_html[ ]
        bundle_zip[ ]

        shinyngs -->|rnaseq,affy,maxquant,geo| shiny_html
        quarto -->|rnaseq,affy,maxquant,geo| report_html
        quarto -->|rnaseq,affy,maxquant,geo| bundle
        bundle -->|rnaseq,affy,maxquant,geo| bundle_zip
    end

    subgraph plots [Plots]
        %%metro entry: left | rnaseq, affy, maxquant, geo
        plot_expl[Exploratory]
        plot_diff[Differential]
        plots_png[ ]

        plot_expl -->|rnaseq,affy,maxquant,geo| plots_png
        plot_diff -->|rnaseq,affy,maxquant,geo| plots_png
    end

    %% Inter-section edges
    matrix_filter -->|rnaseq,affy,maxquant,geo| limma
    matrix_filter -->|rnaseq| deseq2
    matrix_filter -->|rnaseq| dream
    matrix_filter -->|rnaseq| propd
    %% Section 2 -> Section 3 (functional from differential results)
    limma -->|rnaseq,affy,maxquant,geo| gsea
    limma -->|rnaseq,affy,maxquant,geo| gprofiler2
    limma -->|rnaseq,affy,maxquant,geo| decoupler
    limma -->|rnaseq| grea
    %% Section 2 -> Section 4 (plots are parallel, both from differential trunk)
    limma -->|rnaseq,affy,maxquant,geo| plot_expl
    limma -->|rnaseq,affy,maxquant,geo| plot_diff
    %% Section 2/3 -> Section 5 (reporting from differential + functional)
    limma -->|rnaseq,affy,maxquant,geo| shinyngs
    limma -->|rnaseq,affy,maxquant,geo| quarto
    gsea -->|rnaseq,affy,maxquant,geo| quarto
    gprofiler2 -->|rnaseq,affy,maxquant,geo| quarto
    decoupler -->|rnaseq,affy,maxquant,geo| quarto
    grea -->|rnaseq| quarto

CLI command

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

Rendered map

Genomeassembly Staggered

sanger-tol/genomeassembly with explicit `%%metro grid:` directives stacking each section in its own grid row. Regression fixture: cross-column junction routes were going backward in X.

Mermaid source

%%metro title: sanger-tol/genomeassembly
%%metro style: dark
%%metro line: long_reads | Long reads | #3d95fd
%%metro line: hic_reads | Hi-C reads | #FA6863
%%metro line: i10x_reads | 10X reads | #EB7AEB
%%metro line: assemblies | Assembly | #24B064
%%metro file: input_long_reads | FASTX
%%metro file: input_hic_reads | CRAM
%%metro file: input_10x_reads | FASTQ
%%metro grid: raw_asm | 0, 0, 2
%%metro grid: purging | 2, 2, 2
%%metro grid: polishing | 4, 4, 2
%%metro grid: scaffolding | 6, 6, 4
%%metro grid: genome_statistics | 8, 8, 4
%%metro line_order: span
%%metro compact_offsets: true
%%metro legend: bl

graph LR
    subgraph raw_asm [Raw assembly]
        %%metro exit: bottom | hic_reads
        %%metro exit: right | assemblies,long_reads
        input_long_reads[ ]
        input_hic_reads[ ]
        hifiasm[hifiasm]
        input_long_reads -->|long_reads| hifiasm
        input_hic_reads -->|hic_reads| hifiasm
    end
    subgraph purging [Purging]
        %%metro entry: left | assemblies,long_reads
        %%metro exit: right | assemblies
        purging_minimap2[minimap2]
        purge_dups[purge_dups]
        purging_minimap2 -->|assemblies,long_reads| purge_dups
    end
    subgraph polishing [Polishing]
        %%metro entry: left | assemblies
        %%metro exit: right | assemblies
        input_10x_reads[ ]
        longranger[Longranger]
        freebayes[FreeBayes]
        input_10x_reads -->|i10x_reads| longranger
        longranger -->|i10x_reads,assemblies| freebayes
    end
    subgraph scaffolding [Scaffolding]
        %%metro entry: left | assemblies
        %%metro entry: bottom | hic_reads
        %%metro exit: right | assemblies
        scaffolding_bwamem2[bwa-mem2]
        scaffolding_minimap2[minimap2]
        yahs[YaHS]
        pretextmap[PretextMap]
        juicer[Juicer]
        cooler[Cooler]
        scaffolding_bwamem2 -->|assemblies,hic_reads| yahs
        scaffolding_minimap2 -->|assemblies,hic_reads| yahs
        yahs -->|assemblies,hic_reads| pretextmap
        yahs -->|assemblies,hic_reads| juicer
        yahs -->|assemblies,hic_reads| cooler
    end
    subgraph genome_statistics [Genome QC]
        %%metro entry: left | assemblies
        asmstats[asmstats]
        gfastats[GFAStats]
        busco[BUSCO]
        merquryfk[MerquryFK]
        asmstats -->|assemblies| gfastats
        asmstats -->|assemblies| busco
        asmstats -->|assemblies| merquryfk
    end

    %% Inter-section edges
    hifiasm -->|assemblies,long_reads| purging_minimap2
    hifiasm -->|hic_reads| scaffolding_bwamem2
    hifiasm -->|hic_reads| scaffolding_minimap2
    hifiasm -->|assemblies| longranger
    hifiasm -->|assemblies| scaffolding_bwamem2
    hifiasm -->|assemblies| scaffolding_minimap2
    purge_dups -->|assemblies| longranger
    purge_dups -->|assemblies| scaffolding_bwamem2
    purge_dups -->|assemblies| scaffolding_minimap2
    freebayes -->|assemblies| scaffolding_bwamem2
    freebayes -->|assemblies| scaffolding_minimap2
    hifiasm -->|assemblies| asmstats
    purge_dups -->|assemblies| asmstats
    freebayes -->|assemblies| asmstats
    yahs -->|assemblies| asmstats

CLI command

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

Rendered map

Rnaseq Lite

Simplified RNA-seq pipeline with three analysis routes.

Mermaid source

%%metro title: RNA-seq Lite
%%metro style: dark
%%metro line: star | STAR + Salmon | #2db572
%%metro line: hisat | HISAT2 | #f5c542
%%metro line: pseudo | Pseudo-alignment | #e63946

graph LR
    subgraph preprocessing [Pre-processing]
        input[Input]
        fastqc_raw[FastQC]
        fastp[FastP]
        trimgalore[Trim Galore!]
        fastqc_trim[FastQC]
        filter[SortMeRNA]
        fastqc_filt[FastQC]

        input -->|star,hisat,pseudo| fastqc_raw
        fastqc_raw -->|star,hisat,pseudo| fastp
        fastqc_raw -->|star,hisat,pseudo| trimgalore
        fastp -->|star,hisat,pseudo| fastqc_trim
        trimgalore -->|star,hisat,pseudo| fastqc_trim
        fastqc_trim -->|star,hisat,pseudo| filter
        filter -->|star,hisat,pseudo| fastqc_filt
    end

    subgraph genome_align [Genome alignment]
        star_align[STAR]
        hisat_align[HISAT2]
        umi_dedup[UMI-tools dedup]
        salmon_quant[Salmon]
        rsem_quant[featureCounts]

        star_align -->|star| umi_dedup
        hisat_align -->|hisat| umi_dedup
        umi_dedup -->|star| salmon_quant
        umi_dedup -->|hisat| rsem_quant
    end

    subgraph pseudo_align [Pseudo-alignment]
        salmon_pseudo[Salmon]
        tximport[tximport]
        summarized_exp[Sum. Exp.]

        salmon_pseudo -->|pseudo| tximport
        tximport -->|pseudo| summarized_exp
    end

    subgraph postprocessing [Post-processing]
        samtools[SAMtools]
        picard[Picard]
        bedtools[BEDTools]
        bigwig[bedGraphToBigWig]

        samtools -->|star,hisat| picard
        picard -->|star,hisat| bedtools
        bedtools -->|star,hisat| bigwig
    end

    subgraph qc_report [QC & Reporting]
        rseqc[RSeQC]
        dupradar[dupRadar]
        featurecounts[featureCounts]
        multiqc[MultiQC]

        rseqc -->|star,hisat| dupradar
        dupradar -->|star,hisat| featurecounts
        featurecounts -->|star,hisat| multiqc
    end

    fastqc_filt -->|star| star_align
    fastqc_filt -->|hisat| hisat_align
    fastqc_filt -->|pseudo| salmon_pseudo
    salmon_quant -->|star| samtools
    rsem_quant -->|hisat| samtools
    bigwig -->|star,hisat| rseqc

CLI command

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

Rendered map

Variant Calling

Variant calling pipeline with four lines sharing alignment.

Mermaid source

%%metro title: Variant Calling Pipeline
%%metro style: dark
%%metro line: wgs | Whole Genome | #2db572
%%metro line: wes | Whole Exome | #0570b0
%%metro line: panel | Targeted Panel | #f5c542
%%metro line: rna_var | RNA Variants | #e63946

graph LR
    subgraph input_qc [Input & QC]
        input[Input]
        fastqc[FastQC]
        fastp[FastP]
        trimgalore[Trim Galore!]
        fastqc_trim[FastQC]

        input -->|wgs,wes,panel,rna_var| fastqc
        fastqc -->|wgs,wes,panel,rna_var| fastp
        fastqc -->|wgs,wes,panel,rna_var| trimgalore
        fastp -->|wgs,wes,panel,rna_var| fastqc_trim
        trimgalore -->|wgs,wes,panel,rna_var| fastqc_trim
    end

    subgraph alignment [Alignment]
        bwa[BWA-MEM2]
        star_align[STAR]
        samtools[SAMtools sort]
        markdup[MarkDuplicates]
        bqsr[BQSR]

        bwa -->|wgs,wes,panel| samtools
        star_align -->|rna_var| samtools
        samtools -->|wgs,wes,panel,rna_var| markdup
        markdup -->|wgs,wes,panel,rna_var| bqsr
    end

    subgraph dna_calling [DNA Variant Calling]
        haplotypecaller[HaplotypeCaller]
        deepvariant[DeepVariant]
        strelka[Strelka2]
        merge_vcf[Merge VCFs]

        haplotypecaller -->|wgs| merge_vcf
        deepvariant -->|wes| merge_vcf
        strelka -->|panel| merge_vcf
    end

    subgraph rna_calling [RNA Variant Calling]
        splitncigar[SplitNCigar]
        rna_hc[HaplotypeCaller]
        rna_filter[FilterVariants]

        splitncigar -->|rna_var| rna_hc
        rna_hc -->|rna_var| rna_filter
    end

    subgraph annotation [Annotation & Filtering]
        vep[VEP]
        snpsift[SnpSift]
        filter_pass[Filter PASS]

        vep -->|wgs,wes,panel,rna_var| snpsift
        snpsift -->|wgs,wes,panel,rna_var| filter_pass
    end

    subgraph reporting [Reporting]
        bcftools_stats[bcftools stats]
        multiqc[MultiQC]

        bcftools_stats -->|wgs,wes,panel,rna_var| multiqc
    end

    fastqc_trim -->|wgs,wes,panel| bwa
    fastqc_trim -->|rna_var| star_align
    bqsr -->|wgs| haplotypecaller
    bqsr -->|wes| deepvariant
    bqsr -->|panel| strelka
    bqsr -->|rna_var| splitncigar
    merge_vcf -->|wgs,wes,panel| vep
    rna_filter -->|rna_var| vep
    filter_pass -->|wgs,wes,panel,rna_var| bcftools_stats

CLI command

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

Rendered map

Foldback Exit Peeloff

An auto-folded serpentine (`%%metro fold_threshold: 15`) where a return-row section exit splits a bundle to two downstream sections: one line continues level along the row, the other turns down to a lower loop. Regression fixture for the peel-off lane crossover at the exit -- the reversal must follow the continuing line through the peel-off junction so it stays level.

Mermaid source

%%metro title: Fold-back exit peel-off
%%metro style: dark
%%metro fold_threshold: 15
%%metro file: fastq_in | FASTQ
%%metro file: report_out | HTML
%%metro line: dna | DNA (Tumor + Normal) | #4a90d9
%%metro line: rna | RNA (Tumor) | #e63946
%%metro line: realignment | Realignment (RNA) | #f5c542
%%metro line_order: definition
%%metro legend: bl

graph LR
    subgraph preprocessing [Pre-processing & Alignment]
        fastq_in[ ]
        fastqc[FastQC]
        fastp[fastp]
        bwa_mem[BWA-mem/BWA-mem2]
        star[STAR]
        samtools_merge[SAMtools Merge]

        fastq_in -->|dna,rna| fastqc
        fastqc -->|dna,rna| fastp
        fastp -->|dna| bwa_mem
        fastp -->|rna| star
        bwa_mem -->|dna| samtools_merge
        star -->|rna| samtools_merge
    end

    subgraph gatk_preproc [GATK Preprocessing]
        markduplicates[MarkDuplicates]
        splitncigar[SplitNCigarReads]
        baserecalibrator[BaseRecalibrator]
        applybqsr[ApplyBQSR]
        samtools_stats[SAMtools Stats]
        mosdepth[Mosdepth]

        markduplicates -->|dna| baserecalibrator
        markduplicates -->|rna| splitncigar
        splitncigar -->|rna| baserecalibrator
        baserecalibrator -->|dna,rna| applybqsr
        applybqsr -->|dna,rna| samtools_stats
        samtools_stats -->|dna,rna| mosdepth
    end

    subgraph variant_calling [Variant Calling (parallel)]
        vc_fork[ ]
        mutect2[Mutect2]
        strelka[Strelka2]
        sage[SAGE]
        vc_join[ ]

        vc_fork -->|dna,rna| mutect2
        vc_fork -->|dna,rna| strelka
        vc_fork -->|dna,rna| sage
        mutect2 -->|dna,rna| vc_join
        strelka -->|dna,rna| vc_join
        sage -->|dna,rna| vc_join
    end

    subgraph normalization [Normalization & Annotation]
        vt_decompose[VT Decompose]
        vt_normalize[VT Normalize]
        ensemblvep[Ensembl VEP]

        vt_decompose -->|dna,rna| vt_normalize
        vt_normalize -->|dna,rna| ensemblvep
    end

    subgraph consensus [Consensus & Filtering]
        vcf2maf[vcf2MAF]
        run_consensus[Consensus]
        maf_filtering[MAF Filtering]

        vcf2maf -->|dna,rna| run_consensus
        run_consensus -->|dna,rna| maf_filtering
    end

    subgraph realign [Realignment (RNA)]
        maf2bed[MAF2BED]
        extract_reads[Extract Reads]
        hisat2[HISAT2]
        markdup_re[MarkDuplicates]
        splitncigar_re[SplitNCigarReads]
        bqsr_re[BQSR]
        varcall_re[Variant Calling]
        norm_re[Normalization]
        annotate_re[Annotation]
        consensus_re[Consensus]
        filter_re[MAF Filtering]

        maf2bed -->|realignment| extract_reads
        extract_reads -->|realignment| hisat2
        hisat2 -->|realignment| markdup_re
        markdup_re -->|realignment| splitncigar_re
        splitncigar_re -->|realignment| bqsr_re
        bqsr_re -->|realignment| varcall_re
        varcall_re -->|realignment| norm_re
        norm_re -->|realignment| annotate_re
        annotate_re -->|realignment| consensus_re
        consensus_re -->|realignment| filter_re
    end

    subgraph reporting [Reporting]
        rna_filter[RNA MAF Filtering]
        rna_filter -->|rna,realignment| multiqc
        multiqc[MultiQC]
        report_out[ ]

        multiqc -->|rna,realignment| report_out
    end

    %% Inter-section edges
    maf_filtering -->|realignment| maf2bed
    samtools_merge -->|dna,rna| markduplicates
    mosdepth -->|dna,rna| vc_fork
    vc_join -->|dna,rna| vt_decompose
    ensemblvep -->|dna,rna| vcf2maf
    filter_re -->|realignment| rna_filter
    maf_filtering -->|rna| rna_filter

CLI command

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

Rendered map

Rowmate Tb Side Entry Top Align

An auto-folded RNA-seq map whose row-0 Post-processing section is a TB section entered from the left. Regression fixture: the perpendicular entry approach occupies the band above the section's first station, so the content-hug shrink must not drop the section's box top below its feeder row-mate, floating its number badge beneath the rest of the grid row.

Mermaid source

%%metro title: TB side-entry row-mate top alignment
%%metro style: light
%%metro diamond_style: symmetric
%%metro file: fastq_in | FASTQ
%%metro file: report_bowtie2 | HTML
%%metro line: star_rsem | Aligner: STAR, Quantification: RSEM | #0570b0
%%metro line: star_salmon | Aligner: STAR, Quantification: Salmon (default) | #2db572
%%metro line: bowtie2_salmon | Aligner: Bowtie2 (prokaryotic), Quantification: Salmon | #ff8c00
%%metro line: hisat2 | Aligner: HISAT2, Quantification: None | #f5c542
%%metro line: pseudo_salmon | Pseudo-aligner: Salmon, Quantification: Salmon | #e63946
%%metro line: pseudo_kallisto | Pseudo-aligner: Kallisto, Quantification: Kallisto | #7b2d3b
%%metro legend: bl
%%metro logo_scale: 0.85

graph LR
    subgraph preprocessing [Pre-processing]
        %%metro exit: right | star_salmon, star_rsem, hisat2, bowtie2_salmon
        %%metro exit: bottom | pseudo_salmon, pseudo_kallisto
        fastq_in[ ]
        cat_fastq[cat FASTQ]
        fastqc_raw[FastQC]
        umi_tools_extract[UMI-tools Extract]
        fastp[fastp]
        trimgalore[Trim Galore!]
        fastqc_trimmed[FastQC]
        bbsplit[BBSplit]
        sortmerna[SortMeRNA]
        ribodetector[RiboDetector]
        bowtie2_rrna[Bowtie2]
        fastqc_filtered[FastQC]
        infer_strandedness[Infer Strand.]

        fastq_in -->|pseudo_salmon,pseudo_kallisto,star_salmon,star_rsem,hisat2,bowtie2_salmon| cat_fastq
        cat_fastq -->|pseudo_salmon,pseudo_kallisto,star_salmon,star_rsem,hisat2,bowtie2_salmon| fastqc_raw
        fastqc_raw -->|pseudo_salmon,pseudo_kallisto,star_salmon,star_rsem,hisat2,bowtie2_salmon| umi_tools_extract

        umi_tools_extract -->|pseudo_salmon,pseudo_kallisto,star_salmon,star_rsem,hisat2,bowtie2_salmon| fastp
        umi_tools_extract -->|pseudo_salmon,pseudo_kallisto,star_salmon,star_rsem,hisat2,bowtie2_salmon| trimgalore
        fastp -->|pseudo_salmon,pseudo_kallisto,star_salmon,star_rsem,hisat2,bowtie2_salmon| fastqc_trimmed
        trimgalore -->|pseudo_salmon,pseudo_kallisto,star_salmon,star_rsem,hisat2,bowtie2_salmon| fastqc_trimmed

        fastqc_trimmed -->|pseudo_salmon,pseudo_kallisto,star_salmon,star_rsem,hisat2,bowtie2_salmon| bbsplit
        bbsplit -->|pseudo_salmon,pseudo_kallisto,star_salmon,star_rsem,hisat2,bowtie2_salmon| sortmerna
        bbsplit -->|pseudo_salmon,pseudo_kallisto,star_salmon,star_rsem,hisat2,bowtie2_salmon| ribodetector
        bbsplit -->|pseudo_salmon,pseudo_kallisto,star_salmon,star_rsem,hisat2,bowtie2_salmon| bowtie2_rrna
        sortmerna -->|pseudo_salmon,pseudo_kallisto,star_salmon,star_rsem,hisat2,bowtie2_salmon| fastqc_filtered
        ribodetector -->|pseudo_salmon,pseudo_kallisto,star_salmon,star_rsem,hisat2,bowtie2_salmon| fastqc_filtered
        bowtie2_rrna -->|pseudo_salmon,pseudo_kallisto,star_salmon,star_rsem,hisat2,bowtie2_salmon| fastqc_filtered
        fastqc_filtered -->|pseudo_salmon,pseudo_kallisto,star_salmon,star_rsem,hisat2,bowtie2_salmon| infer_strandedness
    end

    subgraph genome_align [Genome alignment & quantification]
        %%metro entry: left | star_salmon, star_rsem, hisat2, bowtie2_salmon
        %%metro exit: right | star_salmon, star_rsem
        %%metro exit: right | hisat2
        star[STAR]
        hisat2_align[HISAT2]
        bowtie2_align[Bowtie2]
        rsem[RSEM]
        salmon_quant[Salmon]
        umi_tools_dedup[UMI-tools Dedup]
        tximport_ga[tximport]
        summarized_exp_ga[Sum. Exp.]
        multiqc_bowtie2[MultiQC]
        report_bowtie2[ ]
        _h1[hidden]
        _h2[hidden]
        _h3[hidden]

        star -->|star_rsem,star_salmon| umi_tools_dedup
        hisat2_align -->|hisat2| umi_tools_dedup
        bowtie2_align -->|bowtie2_salmon| umi_tools_dedup
        umi_tools_dedup -->|star_rsem| rsem
        umi_tools_dedup -->|star_salmon,bowtie2_salmon| salmon_quant
        umi_tools_dedup -->|hisat2| _h1
        _h1 -->|hisat2| _h2
        _h2 -->|hisat2| _h3
        salmon_quant -->|star_salmon,bowtie2_salmon| tximport_ga
        rsem -->|star_rsem| tximport_ga
        tximport_ga -->|star_salmon,star_rsem,bowtie2_salmon| summarized_exp_ga
        summarized_exp_ga -->|bowtie2_salmon| multiqc_bowtie2
        multiqc_bowtie2 -->|bowtie2_salmon| report_bowtie2
    end

    subgraph pseudo_align [Pseudo-alignment & quantification]
        %%metro entry: left | pseudo_salmon, pseudo_kallisto
        salmon_pseudo[Salmon]
        kallisto[Kallisto]
        tximport_pa[tximport]

        salmon_pseudo -->|pseudo_salmon| tximport_pa
        kallisto -->|pseudo_kallisto| tximport_pa
    end

    subgraph postprocessing [Post-processing]
        %%metro direction: TB
        %%metro entry: left | star_salmon, star_rsem, hisat2
        %%metro exit: bottom | star_salmon, star_rsem, hisat2
        picard[Picard]
        bedtools[BEDTools]
        bedgraph[bedGraphToBigWig]
        stringtie[StringTie]

        picard -->|star_salmon,star_rsem,hisat2| bedtools
        bedtools -->|star_salmon,star_rsem,hisat2| bedgraph
        bedgraph -->|star_salmon,star_rsem,hisat2| stringtie
    end


    %% Inter-section edges
    infer_strandedness -->|star_salmon,star_rsem| star
    infer_strandedness -->|hisat2| hisat2_align
    infer_strandedness -->|bowtie2_salmon| bowtie2_align
    infer_strandedness -->|pseudo_salmon| salmon_pseudo
    infer_strandedness -->|pseudo_kallisto| kallisto
    summarized_exp_ga -->|star_salmon,star_rsem| picard
    _h3 -->|hisat2| picard

CLI command

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

Rendered map

Rowmate Tb Side Entry Top Align Grow

A row-0 TB Post-processing section entered from the left sits beside a tall fan section whose box top grows upward to fit a branch above its trunk. Regression fixture: when the feeder row-mate's top grows, the side-entered vertical section must follow it up rather than hugging its low content, keeping its number badge level with the rest of the grid row.

Mermaid source

%%metro title: TB side-entry row-mate top alignment
%%metro line: sa | STAR / Salmon | #2db572
%%metro line: sr | STAR / RSEM | #0570b0
%%metro line: hs | HISAT2 | #f5c542
%%metro line: bt | Bowtie2 (terminates) | #ff8c00
%%metro grid: source | 0,0
%%metro grid: align | 1,0
%%metro grid: post | 2,0

graph LR
    subgraph source [Pre-processing]
        %%metro exit: right | sa, sr, hs, bt
        infer[Infer Strand.]
    end
    subgraph align [Alignment & quantification]
        %%metro entry: left | sa, sr, hs, bt
        %%metro exit: right | sa, sr, hs
        star[STAR]
        hisat[HISAT2]
        bowtie[Bowtie2]
        dedup[Dedup]
        rsem[RSEM]
        salmon[Salmon]
        sumexp[Sum. Exp.]
        star -->|sa,sr| dedup
        hisat -->|hs| dedup
        bowtie -->|bt| dedup
        dedup -->|sr| rsem
        dedup -->|sa,bt| salmon
        dedup -->|hs| sumexp
        rsem -->|sr| sumexp
        salmon -->|sa,bt| sumexp
    end
    subgraph post [Post-processing]
        %%metro direction: TB
        %%metro entry: left | sa, sr, hs
        %%metro exit: bottom | sa, sr, hs
        picard[Picard]
        bedtools[BEDTools]
        bigwig[bigWig]
        stringtie[StringTie]
        picard -->|sa,sr,hs| bedtools
        bedtools -->|sa,sr,hs| bigwig
        bigwig -->|sa,sr,hs| stringtie
    end
    infer -->|sa,sr,hs,bt| star
    sumexp -->|sa,sr,hs| picard

CLI command

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

Rendered map

Seqinspector

nf-core/seqinspector with an explicit `%%metro grid:` stacking two single-row sections (Run Folder, BAM Files) in the column beside a rowspan-2 FASTQ section. Regression fixture: the stacked sections must fill the rowspan band -- the top one's box top meets the band top (instead of a fan poking into the title) and the bottom one's box bottom meets the band bottom (instead of floating high with slack below).

Mermaid source

%%metro title: nf-core/seqinspector
%%metro style: dark
%%metro logo: examples/showcase/nf-core-seqinspector_logo_light.png | examples/showcase/nf-core-seqinspector_logo_dark.png

%%metro line: run_folder | Run Folder | #1f77b4
%%metro line: fastq_files | FASTQ Files | #ff7f0e
%%metro line: bam_files | BAM Files | #24B064

%%metro file: fastq_in | FASTQ | | banner
%%metro dir: rundir_in | RUNDIR
%%metro file: multiqc | HTML | | banner
%%metro center_ports: true
%%metro compact_offsets: true
%%metro legend: bl
%%metro grid: fastq_files | 0,0,2
%%metro grid: run_folder | 1,0
%%metro grid: bam_files | 1,1
%%metro grid: multiqc | 2,0,2

graph LR
    subgraph fastq_files [FASTQ Files]
        fastq_in[ ]

        bbmap[BBMap Clumpify]
        fastp[FastP]
        fastqc[FASTQC]
        fastqe[FASTQE]
        fastqscreen[FastQ Screen]
        fq_lint[FQ Lint]
        kraken2[Kraken2]
        krona[Krona]
        seqfu[SeqFu Stats]
        seqkit[SeqKit Stats]
        seqtk[Seqtk sample]
        sequali[Sequali]
        toulligqc[ToulligQC]

        fastq_in -->|fastq_files| seqtk

        seqtk -->|fastq_files| kraken2
        kraken2 -->|fastq_files| krona

        subgraph bam_files [BAM Files]
            bwamem2[BWAmem2]

            picardhs[Picard collecthsmetrics]
            picardmultiple[Picard collectmultiplemetrics]
            riker[Riker multi]

            bwamem2 -->|bam_files| picardhs
            bwamem2 -->|bam_files| picardmultiple
            bwamem2 -->|bam_files| riker
        end

        seqtk -->|fastq_files| bbmap
        seqtk -->|fastq_files| bwamem2
        seqtk -->|fastq_files| fastp
        seqtk -->|fastq_files| fastqc
        seqtk -->|fastq_files| fastqe
        seqtk -->|fastq_files| fastqscreen
        seqtk -->|fastq_files| fq_lint
        seqtk -->|fastq_files| seqfu
        seqtk -->|fastq_files| seqkit
        seqtk -->|fastq_files| sequali
        seqtk -->|fastq_files| toulligqc
    end

    subgraph run_folder [Run Folder]
        rundir_in[ ]

        checkqc[CheckQC]
        rundirparser[Rundirparser]

        rundir_in -->|run_folder| checkqc
        rundir_in -->|run_folder| rundirparser
    end

    subgraph multiqc [MultiQC]
        multiqc[MultiQC]

        bbmap -->|fastq_files| multiqc
        checkqc -->|run_folder| multiqc
        fastp -->|fastq_files| multiqc
        fastqc -->|fastq_files| multiqc
        fastqe -->|fastq_files| multiqc
        fastqscreen -->|fastq_files| multiqc
        fq_lint -->|fastq_files| multiqc
        krona -->|fastq_files| multiqc
        picardhs -->|bam_files| multiqc
        picardmultiple -->|bam_files| multiqc
        riker -->|bam_files| multiqc
        rundirparser -->|run_folder| multiqc
        seqfu -->|fastq_files| multiqc
        seqkit -->|fastq_files| multiqc
        sequali -->|fastq_files| multiqc
        toulligqc -->|fastq_files| multiqc
    end

CLI command

nf-metro render examples/showcase/seqinspector.mmd -o seqinspector.svg

Rendered map

Basic Topologies

Single Section

One section, one line. The simplest possible case.

Mermaid source

%%metro title: Single Section
%%metro style: dark
%%metro line: main | Main | #e63946

graph LR
    subgraph only [Only Section]
        a[Input]
        b[Process]
        c[Output]
        a -->|main| b
        b -->|main| c
    end

CLI command

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

Rendered map

Deep Linear

Seven sections in a straight chain. Exercises the grid fold threshold.

Mermaid source

%%metro title: Deep Linear Chain
%%metro style: dark
%%metro line: main | Main | #e63946
%%metro line: alt | Alternative | #2db572

graph LR
    subgraph sec1 [Input]
        s1a[Read]
        s1b[Validate]
        s1a -->|main,alt| s1b
    end

    subgraph sec2 [QC]
        s2a[FastQC]
        s2b[MultiQC]
        s2a -->|main,alt| s2b
    end

    subgraph sec3 [Trim]
        s3a[Trim]
        s3b[Filter]
        s3c[Check]
        s3a -->|main| s3b
        s3a -->|alt| s3b
        s3b -->|main,alt| s3c
    end

    subgraph sec4 [Align]
        s4a[Index]
        s4b[Map]
        s4c[Sort]
        s4a -->|main,alt| s4b
        s4b -->|main,alt| s4c
    end

    subgraph sec5 [Quant]
        s5a[Count]
        s5b[Normalize]
        s5a -->|main,alt| s5b
    end

    subgraph sec6 [Analysis]
        s6a[Diff Expr]
        s6b[Pathway]
        s6c[Annotate]
        s6a -->|main,alt| s6b
        s6b -->|main,alt| s6c
    end

    subgraph sec7 [Report]
        s7a[Aggregate]
        s7b[Report]
        s7a -->|main,alt| s7b
    end

    s1b -->|main,alt| s2a
    s2b -->|main,alt| s3a
    s3c -->|main,alt| s4a
    s4c -->|main,alt| s5a
    s5b -->|main,alt| s6a
    s6c -->|main,alt| s7a

CLI command

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

Rendered map

Parallel Independent

Two disconnected pipelines stacked vertically.

Mermaid source

%%metro title: Parallel Independent
%%metro style: dark
%%metro line: dna | DNA Pipeline | #e63946
%%metro line: rna | RNA Pipeline | #0570b0

graph LR
    subgraph dna_input [DNA Input]
        di1[Read DNA]
        di2[QC DNA]
        di1 -->|dna| di2
    end

    subgraph dna_process [DNA Process]
        dp1[Align DNA]
        dp2[Call Variants]
        dp1 -->|dna| dp2
    end

    subgraph rna_input [RNA Input]
        ri1[Read RNA]
        ri2[QC RNA]
        ri1 -->|rna| ri2
    end

    subgraph rna_process [RNA Process]
        rp1[Align RNA]
        rp2[Quantify]
        rp1 -->|rna| rp2
    end

    di2 -->|dna| dp1
    ri2 -->|rna| rp1

CLI command

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

Rendered map

Disconnected Components Fold

A folded disconnected-component layout (`%%metro fold_threshold: 3`). The main trunk folds into a serpentine while a wide standalone section stacks below it. Regression fixture for full clearance between the wide section and the folded trunk's bottom row.

Mermaid source

%%metro title: Disconnected Components (folded)
%%metro style: dark
%%metro fold_threshold: 3
%%metro line: main | Main Pipeline | #e63946
%%metro line: aux | Auxiliary Report | #0570b0

graph LR
    subgraph ingest [Ingest]
        in1[Read Input]
        in2[Validate]
        in1 -->|main| in2
    end

    subgraph process [Process]
        pr1[Align]
        pr2[Filter]
        pr1 -->|main| pr2
    end

    subgraph results [Results]
        re1[Summarise]
        re2[Publish]
        re1 -->|main| re2
    end

    subgraph wide_report [Standalone QC Report]
        w1[Collect]
        w2[Aggregate]
        w3[Annotate]
        w4[Normalise]
        w5[Visualise]
        w6[Export]
        w1 -->|aux| w2
        w2 -->|aux| w3
        w3 -->|aux| w4
        w4 -->|aux| w5
        w5 -->|aux| w6
    end

    in2 -->|main| pr1
    pr2 -->|main| re1

CLI command

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

Rendered map

Mismatched Tracks

Lines with mismatched track counts at shared stations.

Mermaid source

%%metro title: Mismatched Tracks
%%metro style: dark
%%metro line: a | Alpha | #0570b0
%%metro line: b | Beta | #2db572
%%metro line: c | Gamma | #e31a1c
%%metro line: d | Delta | #ff7f00
%%metro line: e | Epsilon | #6a3d9a

graph LR
    subgraph tall [Tall Section]
        t_start[Start]
        t_a[Path A]
        t_b[Path B]
        t_c[Path C]
        t_d[Path D]
        t_e[Path E]
        t_end[End]
        t_start -->|a| t_a
        t_start -->|b| t_b
        t_start -->|c| t_c
        t_start -->|d| t_d
        t_start -->|e| t_e
        t_a -->|a| t_end
        t_b -->|b| t_end
        t_c -->|c| t_end
        t_d -->|d| t_end
        t_e -->|e| t_end
    end

    subgraph short_a [Short A]
        sa1[Proc A]
        sa2[Done A]
        sa1 -->|a| sa2
    end

    subgraph short_b [Short B]
        sb1[Proc B]
        sb2[Done B]
        sb1 -->|b| sb2
    end

    t_end -->|a| sa1
    t_end -->|b| sb1

CLI command

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

Rendered map

Self Crossing Bridge

One colour whose vertical bus crosses its own independent horizontal connector earns a bridge gap (same-colour crossover, not a fan).

Mermaid source

%%metro title: Self-Crossing Bridge
%%metro style: dark
%%metro line: bus | Bus | #0570b0

%%metro grid: top | 0,0
%%metro grid: bus_sink | 0,2
%%metro grid: mid_src | 0,1
%%metro grid: mid_sink | 1,1

graph LR
    subgraph top [Top]
        t1[Top In]
        t2[Top Out]
        t1 -->|bus| t2
    end

    subgraph mid_src [Mid Source]
        m1[Mid In]
        m2[Mid Out]
        m1 -->|bus| m2
    end

    subgraph mid_sink [Mid Sink]
        ms1[Mid Collect]
        ms2[Mid Report]
        ms1 -->|bus| ms2
    end

    subgraph bus_sink [Bus Sink]
        b1[Bus Collect]
        b2[Bus Report]
        b1 -->|bus| b2
    end

    t2 -->|bus| b1
    m2 -->|bus| ms1

CLI command

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

Rendered map

Fan-out and Fan-in

Fork Join Interior Label

A three-way fork-join whose wide middle-branch label sits inside the loop. The loop widens symmetrically so the interior label clears the diverging and reconverging bundles on both sides, keeping the branch centred.

Mermaid source

%%metro title: Fork-join interior label
%%metro diamond_style: symmetric
%%metro line: star_rsem | STAR / RSEM | #0570b0
%%metro line: star_salmon | STAR / Salmon | #2db572
%%metro line: hisat2 | HISAT2 | #f5c542
%%metro line: bowtie2_salmon | Bowtie2 / Salmon | #ff8c00
%%metro line: pseudo_salmon | Salmon | #e63946
%%metro line: pseudo_kallisto | Kallisto | #7b2d3b

graph LR
    subgraph rrna [rRNA removal]
        bbsplit[BBSplit]
        sortmerna[SortMeRNA]
        ribodetector[RiboDetector]
        bowtie2_rrna[Bowtie2]
        fastqc[FastQC]

        bbsplit -->|star_rsem,star_salmon,hisat2,bowtie2_salmon,pseudo_salmon,pseudo_kallisto| sortmerna
        bbsplit -->|star_rsem,star_salmon,hisat2,bowtie2_salmon,pseudo_salmon,pseudo_kallisto| ribodetector
        bbsplit -->|star_rsem,star_salmon,hisat2,bowtie2_salmon,pseudo_salmon,pseudo_kallisto| bowtie2_rrna
        sortmerna -->|star_rsem,star_salmon,hisat2,bowtie2_salmon,pseudo_salmon,pseudo_kallisto| fastqc
        ribodetector -->|star_rsem,star_salmon,hisat2,bowtie2_salmon,pseudo_salmon,pseudo_kallisto| fastqc
        bowtie2_rrna -->|star_rsem,star_salmon,hisat2,bowtie2_salmon,pseudo_salmon,pseudo_kallisto| fastqc
    end

CLI command

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

Rendered map

Wide Fan Out

One source fanning out to four target sections.

Mermaid source

%%metro title: Wide Fan-Out
%%metro style: dark
%%metro line: alpha | Alpha | #e63946
%%metro line: beta | Beta | #2db572
%%metro line: gamma | Gamma | #0570b0
%%metro line: delta | Delta | #f5c542

graph LR
    subgraph source [Source]
        input[Input]
        process[Process]
        input -->|alpha,beta,gamma,delta| process
    end

    subgraph target_a [Target A]
        a1[Step A1]
        a2[Step A2]
        a1 -->|alpha| a2
    end

    subgraph target_b [Target B]
        b1[Step B1]
        b2[Step B2]
        b1 -->|beta| b2
    end

    subgraph target_c [Target C]
        c1[Step C1]
        c2[Step C2]
        c1 -->|gamma| c2
    end

    subgraph target_d [Target D]
        d1[Step D1]
        d2[Step D2]
        d1 -->|delta| d2
    end

    process -->|alpha| a1
    process -->|beta| b1
    process -->|gamma| c1
    process -->|delta| d1

CLI command

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

Rendered map

Wide Fan In

Four sources converging into one target section.

Mermaid source

%%metro title: Wide Fan-In
%%metro style: dark
%%metro line: alpha | Alpha | #e63946
%%metro line: beta | Beta | #2db572
%%metro line: gamma | Gamma | #0570b0
%%metro line: delta | Delta | #f5c542

graph LR
    subgraph src_a [Source A]
        a1[Step A1]
        a2[Step A2]
        a1 -->|alpha| a2
    end

    subgraph src_b [Source B]
        b1[Step B1]
        b2[Step B2]
        b1 -->|beta| b2
    end

    subgraph src_c [Source C]
        c1[Step C1]
        c2[Step C2]
        c1 -->|gamma| c2
    end

    subgraph src_d [Source D]
        d1[Step D1]
        d2[Step D2]
        d1 -->|delta| d2
    end

    subgraph sink [Sink]
        merge[Merge]
        output[Output]
        merge -->|alpha,beta,gamma,delta| output
    end

    a2 -->|alpha| merge
    b2 -->|beta| merge
    c2 -->|gamma| merge
    d2 -->|delta| merge

CLI command

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

Rendered map

Section Diamond

Section-level fork-join: fan-out then reconverge.

Mermaid source

%%metro title: Section Diamond
%%metro style: dark
%%metro line: left_path | Left Path | #e63946
%%metro line: right_path | Right Path | #0570b0

graph LR
    subgraph start [Start]
        input[Input]
        prep[Prepare]
        input -->|left_path,right_path| prep
    end

    subgraph branch_left [Branch Left]
        l1[Left Step 1]
        l2[Left Step 2]
        l3[Left Step 3]
        l1 -->|left_path| l2
        l2 -->|left_path| l3
    end

    subgraph branch_right [Branch Right]
        r1[Right Step 1]
        r2[Right Step 2]
        r1 -->|right_path| r2
    end

    subgraph finish [Finish]
        merge[Merge]
        report[Report]
        merge -->|left_path,right_path| report
    end

    prep -->|left_path| l1
    prep -->|right_path| r1
    l3 -->|left_path| merge
    r2 -->|right_path| merge

CLI command

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

Rendered map

Uneven Diamond

Node-level fork-join whose branches differ in length; each branch holds its own track instead of collapsing the shorter ones together.

Mermaid source

%%metro title: Uneven fork-join diamond
%%metro line: a | A | #f0a000 | solid
%%metro line: b | B | #3a86ff | solid
%%metro line: c | C | #2bb673 | solid
graph LR
    hub[Hub] -->|a| la[Leaf A]
    hub -->|b| lb[Leaf B]
    lb  -->|b| lb2[Leaf B2]
    hub -->|c| lc[Leaf C]
    la  -->|a| sink[Sink]
    lb2 -->|b| sink
    lc  -->|c| sink

CLI command

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

Rendered map

Symmetric Diamond Beside Wide Fan

A `diamond_style: symmetric` 2-way fork-join sharing a section with a wider 3-way fan. The 2-way diamond straddles its trunk evenly, but at full pitch -- as tall as the 3-way fan, with an empty trunk row between its branches -- because the half-pitch compaction is a per-section decision the mixed-fan section cannot qualify for (#1076).

Mermaid source

%%metro title: Symmetric diamond beside a wider fan
%%metro diamond_style: symmetric
%%metro line: l1 | Route 1 | #0570b0
%%metro line: l2 | Route 2 | #2db572
%%metro line: l3 | Route 3 | #f5c542
%%metro line: l4 | Route 4 | #ff8c00
%%metro line: l5 | Route 5 | #e63946
%%metro line: l6 | Route 6 | #7b2d3b

graph LR
    subgraph prep [Pre-processing]
        extract[Extract]
        toolA[Tool A]
        toolB[Tool B]
        qc[QC]
        splitA[Split A]
        splitB[Split B]
        splitC[Split C]
        qc2[QC]

        extract -->|l1,l2,l3,l4,l5,l6| toolA
        extract -->|l1,l2,l3,l4,l5,l6| toolB
        toolA -->|l1,l2,l3,l4,l5,l6| qc
        toolB -->|l1,l2,l3,l4,l5,l6| qc

        qc -->|l1,l2,l3,l4,l5,l6| splitA
        qc -->|l1,l2,l3,l4,l5,l6| splitB
        qc -->|l1,l2,l3,l4,l5,l6| splitC
        splitA -->|l1,l2,l3,l4,l5,l6| qc2
        splitB -->|l1,l2,l3,l4,l5,l6| qc2
        splitC -->|l1,l2,l3,l4,l5,l6| qc2
    end

CLI command

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

Rendered map

Symmetric Multiline Merge Median

Three metro lines on distinct tracks converging on one shared station under `diamond_style: symmetric`. The merge anchors on the median feeder track (the middle line) rather than the first-declared line's extreme track, so each feeder bends toward it by the least amount (#1277).

Mermaid source

%%metro title: Symmetric multi-line merge
%%metro diamond_style: symmetric
%%metro line: top | Top | #f5c542
%%metro line: mid | Mid | #0570b0
%%metro line: bottom | Bottom | #ff8c00

graph LR
    subgraph section1 [Section]
        %%metro entry: left | top, mid, bottom
        node_top[Top]
        node_mid[Mid]
        node_bottom[Bottom]
        merge[Merge]

        node_top -->|top| merge
        node_mid -->|mid| merge
        node_bottom -->|bottom| merge
    end

CLI command

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

Rendered map

Terminal Symmetric Fan

A terminal section whose entry fans into equal-rank sinks; the fan stays symmetric about the entry port (regression lock for top-anchored terminal fans).

Mermaid source

%%metro title: Terminal Fan
%%metro style: dark
%%metro center_ports: true
%%metro line: a | A | #e63946
%%metro line: b | B | #0570b0

%%metro grid: source | 0,0
%%metro grid: reporting | 1,0

graph LR
    subgraph source [Source]
        s1[Input]
        s2[Process]
        s1 -->|a,b| s2
    end

    subgraph reporting [Reporting]
        %%metro entry: left | a, b
        shiny[Shiny]
        multiqc[MultiQC]
        quarto[Quarto]
    end

    s2 -->|a,b| shiny
    s2 -->|a,b| multiqc
    s2 -->|a,b| quarto

CLI command

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

Rendered map

Internal Source Equal Sibling 2Fan

An internal source station feeds exactly two equal-sibling branches (same line, same downstream join). The source is centred between its two consumers, which straddle it symmetrically, rather than staying collinear with one branch while the other peels off (#1223).

Mermaid source

%%metro title: Internal-source equal-sibling 2-fan
%%metro center_ports: true

graph LR
    subgraph run_folder [Run Folder]
        rundir_in[ ]
        checkqc[CheckQC]
        rundirparser[Rundirparser]
        rundir_in -->|run_folder| checkqc
        rundir_in -->|run_folder| rundirparser
    end
    subgraph sink [Aggregate]
        out[MultiQC]
        checkqc -->|run_folder| out
        rundirparser -->|run_folder| out
    end

CLI command

nf-metro render examples/topologies/internal_source_equal_sibling_2fan.mmd -o internal_source_equal_sibling_2fan.svg

Rendered map

Trunk Through Fan

A pass-through section: the trunk runs straight through a symmetric fan-and-reconverge, exit on the merge row (regression lock for detached reconvergence exits).

Mermaid source

%%metro title: Trunk Through Fan
%%metro style: dark
%%metro center_ports: true
%%metro line: a | A | #e63946
%%metro line: b | B | #0570b0

%%metro grid: source | 0,0
%%metro grid: middle | 1,0
%%metro grid: sink | 2,0

graph LR
    subgraph source [Source]
        s1[Input]
        s2[Prepare]
        s1 -->|a,b| s2
    end

    subgraph middle [Middle]
        %%metro entry: left | a, b
        %%metro exit: right | a, b
        split[Split]
        up[Path Up]
        down[Path Down]
        join[Join]
        split -->|a,b| up
        split -->|a,b| down
        up -->|a,b| join
        down -->|a,b| join
    end

    subgraph sink [Sink]
        %%metro entry: left | a, b
        report[Report]
    end

    s2 -->|a,b| split
    join -->|a,b| report

CLI command

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

Rendered map

Wide Label Fan

A two-column fan whose station labels are wider than the column pitch; the engine wraps the labels and widens spacing so they don't collide.

Mermaid source

%%metro title: Wide Label Fan
%%metro style: dark
%%metro center_ports: true
%%metro line: a | A | #e63946
%%metro line: b | B | #0570b0

graph LR
    subgraph proc [Reporting]
        %%metro entry: left | a, b
        hub[Aggregate]
        align[Alignment Summary]
        quant[Quantification Report]
        aqc[Alignment QC HTML]
        qqc[Quantification QC HTML]
        hub -->|a| align
        hub -->|b| quant
        align -->|a| aqc
        quant -->|b| qqc
    end

CLI command

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

Rendered map

Wrapped Label Trunk

A wrapped station label on a lower track whose block would grow into the metro line on the track above; the label is pulled back to its un-pushed anchor so the name clears the line.

Mermaid source

%%metro title: Wrapped label overlaps track above
%%metro line: qc    | Quality control | #f0a000 | solid
%%metro line: align | Alignment       | #3a86ff | solid
%%metro line: quant | Quantification  | #2bb673 | solid
graph LR
    input[Samplesheet] -->|qc,align,quant| trim[Trim Galore]
    trim -->|qc| fastqc[FastQC]
    trim -->|align,quant| index[Genome index]
    index -->|align| star[STAR]
    star -->|align| sort[Samtools sort]
    index -->|quant| salmon[Salmon]
    fastqc -->|qc| multiqc[MultiQC]
    sort -->|align| multiqc
    salmon -->|quant| multiqc

CLI command

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

Rendered map

Funcprofiler Upstream

A profiling section whose stacked tools share a fan-in/fan-out: a line the 'FMH FunProfiler' station does not carry would rake its wide below-station label, so the label flips to its clear side and the diagonal no longer strikes the glyphs.

Mermaid source

%%metro title: nf-core/funcprofiler (upstream)
%%metro style: dark
%%metro line: qc | Preprocessing & QC | #4CAF50
%%metro line: concat | Merge & Concat | #2196F3
%%metro line: db | Database Prep | #607D8B
%%metro line: humann3 | HUMAnN v3 | #FF9800
%%metro line: humann4 | HUMAnN v4 | #FF5722
%%metro line: fmhfunprofiler | FMH FunProfiler | #E91E63
%%metro line: rgi | RGI | #CDDC39
%%metro line: mifaser | mifaser | #00BCD4
%%metro line: diamond | DIAMOND | #9C27B0
%%metro line: eggnog | eggNOG-mapper | #3F51B5
%%metro line: multiqc | Reporting | #795548
%%metro compact_offsets: true

graph LR
    subgraph input[Input]
        input_short([Short Reads])
        input_dbs([Input Databases])
        sr_qc(Preprocess)
        merge(MERGE_RUNS)
    end

    subgraph profiling[Functional Profiling]
        humann3(HUMAnN v3)
        humann4(HUMAnN v4)
        fmhfunprofiler(FMH FunProfiler)
        RGI(RGI)
        mifaser(mifaser)
        diamond(DIAMOND)
        eggnog_mapper(eggNOG-mapper)
    end

    subgraph QC[Quality Check]
        multiqc(MultiQC)
    end

    subgraph Output[Output]
        output([Results Directory])
    end

    %% DB Prep
    input_dbs -->|db| humann3
    input_dbs -->|db| humann4
    input_dbs -->|db| fmhfunprofiler
    input_dbs -->|db| RGI
    input_dbs -->|db| mifaser
    input_dbs -->|db| diamond
    input_dbs -->|db| eggnog_mapper

    %% Preprocessing
    input_short -->|qc| sr_qc
    sr_qc -->|concat| merge

    %% Profiling split
    merge -->|humann3| humann3
    merge -->|humann4| humann4
    merge -->|fmhfunprofiler| fmhfunprofiler
    merge -->|rgi| RGI
    merge -->|mifaser| mifaser
    merge -->|diamond| diamond
    merge -->|eggnog| eggnog_mapper

    %% Reporting
    sr_qc -->|multiqc| multiqc
    humann3 -->|multiqc| multiqc
    humann4 -->|multiqc| multiqc
    fmhfunprofiler -->|multiqc| multiqc
    RGI -->|multiqc| multiqc
    mifaser -->|multiqc| multiqc
    diamond -->|multiqc| multiqc
    eggnog_mapper -->|multiqc| multiqc

    %% Output
    multiqc -->|multiqc| output
    humann3 -->|humann3| output
    humann4 -->|humann4| output
    fmhfunprofiler -->|fmhfunprofiler| output
    RGI -->|rgi| output
    mifaser -->|mifaser| output
    diamond -->|diamond| output
    eggnog_mapper -->|eggnog| output

CLI command

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

Rendered map

Branching and Multipath

Asymmetric Tree

One root branching into three paths of different depths.

Mermaid source

%%metro title: Asymmetric Tree
%%metro style: dark
%%metro line: short | Short Branch | #e63946
%%metro line: medium | Medium Branch | #2db572
%%metro line: long | Long Branch | #0570b0

graph LR
    subgraph root [Root]
        input[Input]
        dispatch[Dispatch]
        input -->|short,medium,long| dispatch
    end

    subgraph branch_short [Short]
        s1[Quick]
        s2[Result]
        s1 -->|short| s2
    end

    subgraph branch_med_1 [Medium Step 1]
        m1[Medium A]
        m2[Medium B]
        m1 -->|medium| m2
    end

    subgraph branch_med_2 [Medium Step 2]
        m3[Medium C]
        m4[Medium D]
        m3 -->|medium| m4
    end

    subgraph branch_long_1 [Long Step 1]
        l1[Long A]
        l2[Long B]
        l1 -->|long| l2
    end

    subgraph branch_long_2 [Long Step 2]
        l3[Long C]
        l4[Long D]
        l3 -->|long| l4
    end

    subgraph branch_long_3 [Long Step 3]
        l5[Long E]
        l6[Long F]
        l5 -->|long| l6
    end

    dispatch -->|short| s1
    dispatch -->|medium| m1
    dispatch -->|long| l1
    m2 -->|medium| m3
    l2 -->|long| l3
    l4 -->|long| l5

CLI command

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

Rendered map

Complex Multipath

Four lines taking different routes through six sections.

Mermaid source

%%metro title: Complex Multipath
%%metro style: dark
%%metro line: fast | Fast Path | #e63946
%%metro line: standard | Standard Path | #2db572
%%metro line: detailed | Detailed Analysis | #0570b0
%%metro line: legacy | Legacy Path | #f5c542

graph LR
    subgraph input_sec [Input]
        raw[Raw Data]
        validate[Validate]
        raw -->|fast,standard,detailed,legacy| validate
    end

    subgraph fast_track [Fast Track]
        quick_align[Quick Align]
        quick_quant[Quick Quant]
        quick_align -->|fast| quick_quant
    end

    subgraph full_preprocess [Full Pre-process]
        trim[Trim]
        filter[Filter]
        qc_check[QC Check]
        trim -->|standard,detailed,legacy| filter
        filter -->|standard,detailed,legacy| qc_check
    end

    subgraph standard_analysis [Standard Analysis]
        align[Align]
        quant[Quantify]
        align -->|standard,legacy| quant
    end

    subgraph deep_analysis [Deep Analysis]
        hq_align[HQ Align]
        dedup[Dedup]
        hq_quant[HQ Quantify]
        hq_align -->|detailed| dedup
        dedup -->|detailed| hq_quant
    end

    subgraph output_sec [Output]
        aggregate[Aggregate]
        report[Report]
        aggregate -->|fast,standard,detailed,legacy| report
    end

    validate -->|fast| quick_align
    validate -->|standard,detailed,legacy| trim
    qc_check -->|standard,legacy| align
    qc_check -->|detailed| hq_align
    quick_quant -->|fast| aggregate
    quant -->|standard,legacy| aggregate
    hq_quant -->|detailed| aggregate

CLI command

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

Rendered map

Interchange Lane Reorder

Two lanes share one step while a third lane is declared between them. Auto-layout reorders the interleaving lane to an outer track so the two members become adjacent and infer a clean interchange, instead of abstaining (issue #779).

Mermaid source

%%metro title: Interchange lane reorder
%%metro style: dark
%%metro line: top | Top | #d62728
%%metro line: mid | Mid | #2db572
%%metro line: bot | Bot | #f5c542

graph LR
    subgraph s [Parallel lanes]
        top_in[ ]
        mid_in[ ]
        bot_in[ ]
        hub[Shared step]
        mid_step[Mid step]
        top_out[ ]
        mid_out[ ]
        bot_out[ ]
        top_in -->|top| hub
        bot_in -->|bot| hub
        mid_in -->|mid| mid_step
        hub -->|top| top_out
        hub -->|bot| bot_out
        mid_step -->|mid| mid_out
    end

CLI command

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

Rendered map

Multi-line Bundles

Multi Line Bundle

Six lines travelling through the same three-section chain.

Mermaid source

%%metro title: Multi-Line Bundle
%%metro style: dark
%%metro line: line1 | Line 1 | #e63946
%%metro line: line2 | Line 2 | #2db572
%%metro line: line3 | Line 3 | #0570b0
%%metro line: line4 | Line 4 | #f5c542
%%metro line: line5 | Line 5 | #ff8c00
%%metro line: line6 | Line 6 | #7b2d3b

graph LR
    subgraph input_sec [Input]
        raw[Raw]
        qc[QC]
        raw -->|line1,line2,line3,line4,line5,line6| qc
    end

    subgraph process_sec [Processing]
        align[Align]
        sort[Sort]
        dedup[Dedup]
        align -->|line1,line2,line3,line4,line5,line6| sort
        sort -->|line1,line2,line3,line4,line5,line6| dedup
    end

    subgraph output_sec [Output]
        quant[Quantify]
        report[Report]
        quant -->|line1,line2,line3,line4,line5,line6| report
    end

    qc -->|line1,line2,line3,line4,line5,line6| align
    dedup -->|line1,line2,line3,line4,line5,line6| quant

CLI command

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

Rendered map

Mixed Port Sides

A section with both RIGHT and BOTTOM exits.

Mermaid source

%%metro title: Mixed Port Sides
%%metro style: dark
%%metro line: horizontal | Horizontal Flow | #e63946
%%metro line: vertical | Vertical Flow | #0570b0

graph LR
    subgraph origin [Origin]
        start[Start]
        fork[Fork]
        start -->|horizontal,vertical| fork
    end

    subgraph right_sec [Right Section]
        r1[Right A]
        r2[Right B]
        r1 -->|horizontal| r2
    end

    subgraph bottom_sec [Bottom Section]
        b1[Bottom A]
        b2[Bottom B]
        b1 -->|vertical| b2
    end

    fork -->|horizontal| r1
    fork -->|vertical| b1

CLI command

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

Rendered map

Compact Hidden Passthrough

Compact mode keeps a hidden single-line pass-through station on its bundle slot so the two lines weave consistently through the section.

Mermaid source

%%metro title: Hidden Pass-through Compact
%%metro style: dark
%%metro compact_offsets: true
%%metro line: a | Line A | #e63946
%%metro line: b | Line B | #0570b0

graph LR
    subgraph src [Source]
        s1[Input A]
        s2[Input B]
    end

    subgraph process [Process]
        _pass[hidden]
        p1[Step A]
        p2[Step B]
        _pass -->|a| p1
        p1 -->|a,b| p2
    end

    subgraph report [Report]
        r1[Report]
    end

    s1 -->|a| _pass
    s2 -->|b| p1
    p2 -->|a,b| r1

CLI command

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

Rendered map

Compact Gap Peer Conflict

A fork-join whose hub carries non-consecutive offset slots safely abandons gap-compaction when a visible same-layer peer carries the intervening line, rather than cascading the reorder.

Mermaid source

%%metro title: Compaction Gap Peer Conflict
%%metro style: dark
%%metro line: alpha | Alpha | #e63946
%%metro line: beta | Beta | #2db572
%%metro line: gamma | Gamma | #0570b0

graph LR
    subgraph src [Source]
        s1[Input]
        s1 -->|alpha,beta,gamma| s2
        s2[Prepare]
    end

    subgraph proc [Process]
        %%metro entry: left | alpha, beta, gamma
        %%metro exit: right | alpha, beta, gamma
        p1[Fork]
        p2[Alpha Gamma]
        p3[Beta Node]
        p4[Merge]
        p1 -->|alpha,gamma| p2
        p1 -->|beta| p3
        p2 -->|alpha,gamma| p4
        p3 -->|beta| p4
    end

    subgraph sink [Sink]
        t1[End]
    end

    s2 -->|alpha,beta,gamma| p1
    p4 -->|alpha,beta,gamma| t1

CLI command

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

Rendered map

Bundle Terminator Continuation

A two-line bundle enters a station where one line terminates while the other continues to a single successor. The successor holds the trunk row rather than dropping to its own line base, so the chain runs flat instead of dipping into a V-kink before the section exit.

Mermaid source

%%metro title: Bundle Terminator Continuation
%%metro style: dark
%%metro line: qc | QC | #2dd4bf
%%metro line: main | Main | #c792ea

graph LR
    subgraph proc [Processing]
        fastqc[FastQC]
        trim[Trim]
        align[Align]
        fastqc -->|qc,main| trim
        trim -->|main| align
    end

CLI command

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

Rendered map

Aligner Row Terminator Lane Gap

Four aligner lines enter a section together, but one (Bowtie2/Salmon) peels off to MultiQC and terminates inside the section instead of reaching its shared exit port. HISAT2, which does exit, sits on a contiguous offset there rather than inheriting a gap reserved for the terminated line, so its connector into the next section runs level instead of kinking into a short diagonal (issue #1263).

Mermaid source

%%metro title: Aligner row vs pinned continuation
%%metro line: star_rsem | STAR/RSEM | #0570b0
%%metro line: star_salmon | STAR/Salmon | #2db572
%%metro line: bowtie2_salmon | Bowtie2/Salmon | #ff8c00
%%metro line: hisat2 | HISAT2 | #f5c542

graph LR
    subgraph preproc [Pre-processing]
        %%metro exit: right | star_salmon, star_rsem, hisat2, bowtie2_salmon
        fastqc_filtered[FastQC]
    end

    subgraph genome_align [Genome alignment & quantification]
        %%metro entry: left | star_salmon, star_rsem, hisat2, bowtie2_salmon
        %%metro exit: right | star_salmon, star_rsem
        %%metro exit: right | hisat2
        star[STAR]
        hisat2_align[HISAT2]
        bowtie2_align[Bowtie2]
        rsem[RSEM]
        salmon_quant[Salmon]
        umi_tools_dedup[UMI-tools Dedup]
        tximport_ga[tximport]
        summarized_exp_ga[Sum. Exp.]
        multiqc_bowtie2[MultiQC]
        report_bowtie2[ ]
        _h1[hidden]
        _h2[hidden]
        _h3[hidden]

        star -->|star_rsem,star_salmon| umi_tools_dedup
        hisat2_align -->|hisat2| umi_tools_dedup
        bowtie2_align -->|bowtie2_salmon| umi_tools_dedup
        umi_tools_dedup -->|star_rsem| rsem
        umi_tools_dedup -->|star_salmon| salmon_quant
        umi_tools_dedup -->|hisat2| _h1
        _h1 -->|hisat2| _h2
        _h2 -->|hisat2| _h3
        salmon_quant -->|star_salmon| tximport_ga
        rsem -->|star_rsem| tximport_ga
        tximport_ga -->|star_salmon,star_rsem| summarized_exp_ga
        umi_tools_dedup -->|bowtie2_salmon| salmon_quant
        salmon_quant -->|bowtie2_salmon| multiqc_bowtie2
        multiqc_bowtie2 -->|bowtie2_salmon| report_bowtie2
    end

    subgraph postproc [Post-processing]
        %%metro direction: TB
        %%metro entry: left | star_salmon, star_rsem, hisat2
        samtools[SAMtools]
        picard[Picard]

        samtools -->|star_salmon,star_rsem,hisat2| picard
    end

    fastqc_filtered -->|star_salmon,star_rsem| star
    fastqc_filtered -->|hisat2| hisat2_align
    fastqc_filtered -->|bowtie2_salmon| bowtie2_align
    summarized_exp_ga -->|star_salmon,star_rsem| samtools
    _h3 -->|hisat2| samtools

CLI command

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

Rendered map

TB / BT Sections

Bt Chain

A `%%metro direction: BT` (bottom-to-top) section: a three-station chain whose flow runs up the column, the vertical mirror of a TB chain (#1044).

Mermaid source

%%metro title: BT Chain
%%metro style: dark
%%metro line: a | A | #e63946

graph LR
    subgraph work [Work]
        %%metro direction: BT
        w1[First]
        w2[Second]
        w3[Third]
        w1 -->|a| w2
        w2 -->|a| w3
    end

CLI command

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

Rendered map

Bt Fork

A symmetric fan-out inside a `%%metro direction: BT` section: the hub sits at the bottom and both branches fan upward, the lane bundle riding the `+x` side as the rotation image of a TB fork (#1044).

Mermaid source

%%metro title: BT Fork
%%metro style: dark
%%metro line: a | A | #e63946
%%metro line: b | B | #0570b0

graph LR
    subgraph work [Work]
        %%metro direction: BT
        hub[Demux]
        left[Lane A]
        right[Lane B]
        hub -->|a,b| left
        hub -->|a,b| right
    end

CLI command

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

Rendered map

Bt Perp Entry Below

A BT section fed from below: a lower BT section's trailing TOP exit continues up the shared lane into an upper BT section's BOTTOM entry, a two-line bundle riding one column across the seam (#1044).

Mermaid source

%%metro title: BT Fed From Below
%%metro style: dark
%%metro line: a | A | #e63946
%%metro line: b | B | #0570b0

%%metro grid: top_sec | 0,0
%%metro grid: bot_sec | 0,1

graph LR
    subgraph top_sec [Upper]
        %%metro direction: BT
        %%metro entry: bottom | a,b
        t1[Refine]
        t2[Report]
        t1 -->|a,b| t2
    end

    subgraph bot_sec [Lower]
        %%metro direction: BT
        b1[Ingest]
        b2[Clean]
        b1 -->|a,b| b2
    end

    b2 -->|a,b| t1

CLI command

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

Rendered map

Bt Exit Top Above

A BT section's trailing TOP exit dropping up into the BOTTOM entry of an LR section stacked above it (#1044).

Mermaid source

%%metro title: BT Exit Top Into Section Above
%%metro style: dark
%%metro line: a | A | #e63946

%%metro grid: dst_sec | 0,0
%%metro grid: work | 0,1

graph LR
    subgraph dst_sec [Output]
        %%metro direction: LR
        %%metro entry: bottom | a
        o1[Report]
        o2[Archive]
        o1 -->|a| o2
    end

    subgraph work [Work]
        %%metro direction: BT
        %%metro exit: top | a
        w1[Process]
        w2[Collect]
        w1 -->|a| w2
    end

    w2 -->|a| o1

CLI command

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

Rendered map

Bt Exit Top Above 2Line

The two-line form of the BT TOP-exit drop into an LR BOTTOM entry: the bundle keeps its lane across the perpendicular boundary, the BT feeder fanning +x rather than the downward-TB -x (#1066).

Mermaid source

%%metro title: BT Exit Top Into Section Above (2 lines)
%%metro style: dark
%%metro line: a | A | #e63946
%%metro line: b | B | #0570b0

%%metro grid: dst_sec | 0,0
%%metro grid: work | 0,1

graph LR
    subgraph dst_sec [Output]
        %%metro direction: LR
        %%metro entry: bottom | a,b
        o1[Report]
        o2[Archive]
        o1 -->|a,b| o2
    end

    subgraph work [Work]
        %%metro direction: BT
        %%metro exit: top | a,b
        w1[Process]
        w2[Collect]
        w1 -->|a,b| w2
    end

    w2 -->|a,b| o1

CLI command

nf-metro render examples/topologies/bt_exit_top_above_2line.mmd -o bt_exit_top_above_2line.svg

Rendered map

Bt To Lr

A BT section's trailing TOP (perpendicular) exit taking the up-and-over corridor into the LEFT entry of a neighbouring LR section, a two-line bundle staying parallel across the seam (#1044).

Mermaid source

%%metro title: BT Perp Exit Into LR
%%metro style: dark
%%metro line: a | A | #e63946
%%metro line: b | B | #0570b0

%%metro grid: work | 0,0
%%metro grid: out_sec | 1,0

graph LR
    subgraph work [Work]
        %%metro direction: BT
        %%metro exit: top | a,b
        w1[Demux]
        w2[Merge]
        w1 -->|a,b| w2
    end

    subgraph out_sec [Output]
        %%metro direction: LR
        %%metro entry: left | a,b
        o1[Publish]
        o2[Notify]
        o1 -->|a,b| o2
    end

    w2 -->|a,b| o1

CLI command

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

Rendered map

Bt To Tb

A BT section's RIGHT exit feeding a TB section's LEFT entry: an upward flow handing off to a downward one across the column seam (#1044).

Mermaid source

%%metro title: BT Into TB
%%metro style: dark
%%metro line: a | A | #e63946
%%metro line: b | B | #0570b0

%%metro grid: up_sec | 0,0
%%metro grid: down_sec | 1,0

graph LR
    subgraph up_sec [Ascend]
        %%metro direction: BT
        %%metro exit: right | a,b
        u1[Collect]
        u2[Reduce]
        u1 -->|a,b| u2
    end

    subgraph down_sec [Descend]
        %%metro direction: TB
        %%metro entry: left | a,b
        d1[Split]
        d2[Emit]
        d1 -->|a,b| d2
    end

    u2 -->|a,b| d1

CLI command

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

Rendered map

Tb Fork Lane Transpose

A vertical-flow (TB) section whose trunk station forks one line down to an in-section file terminus and the other out to a side exit through a bypass helper. The bypassing line rides the section's lane side of the trunk, so its fork leg reaches the bypass without crossing the straight-down terminus leg (issue #1163).

Mermaid source

%%metro title: TB Fork Lane Transpose
%%metro style: dark
%%metro file: vcf_out | VCF
%%metro line: main | Main | #2db572
%%metro line: qc | QC | #0570b0

graph LR
    subgraph prep [Prep]
        in0[ ]
        align[Align]
        in0 -->|main| align
    end
    subgraph calling [Calling]
        %%metro direction: TB
        caller1[Caller A]
        caller2[Caller B]
        stats[Stats]
        vcf_out[ ]
        caller1 -->|main| stats
        caller2 -->|main| stats
        stats -->|main| vcf_out
    end
    subgraph report [Report]
        mqc[MultiQC]
    end
    align -->|main| caller1
    align -->|main| caller2
    stats -->|qc| mqc

CLI command

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

Rendered map

Tb Passthrough Trunk

A three-line bundle running straight down a linear chain of stations in a `%%metro direction: TB` section. The trunk passes through each station as a clean vertical column: every line holds one offset, so no station reads as an elbow.

Mermaid source

%%metro title: TB pass-through trunk
%%metro style: dark
%%metro line: rna | RNA-seq | #1f9e89
%%metro line: affy | Affymetrix | #e6550d
%%metro line: mq | MaxQuant | #0570b0

%%metro file: bundle_zip | ZIP | Bundle

graph LR
    subgraph analysis [Analysis]
        align[Align]
        call[Call]
        align -->|rna,affy,mq| call
    end

    subgraph reporting [Reporting]
        %%metro direction: TB
        %%metro entry: left | rna, affy, mq
        collect[Collect]
        annotate[Annotate]
        package[Package]
        bundle_zip[ ]

        collect -->|rna,affy,mq| annotate
        annotate -->|rna,affy,mq| package
        package -->|rna,affy,mq| bundle_zip
    end

    call -->|rna,affy,mq| collect

CLI command

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

Rendered map

Tb Internal Diagonal

A symmetric fan-out inside a `%%metro direction: TB` section: the hub centres over its two branch stations, which sit on X tracks either side of it, so both internal edges route as 45-degree diagonals (the `_route_tb_internal` diagonal arm) (#917).

Mermaid source

%%metro title: TB Internal Diagonal
%%metro style: dark
%%metro line: a | A | #e63946
%%metro line: b | B | #0570b0
%%metro grid: source | 0,0
%%metro grid: work | 1,0

graph LR
    subgraph source [Source]
        s1[Start]
        s2[End]
        s1 -->|a,b| s2
    end
    subgraph work [Work]
        %%metro direction: TB
        %%metro entry: top | a,b
        hub[Demux]
        left[Lane A]
        right[Lane B]
        hub -->|a,b| left
        hub -->|a,b| right
    end
    s2 -->|a,b| hub

CLI command

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

Rendered map

Tb Trunk Through Fan

An asymmetric fan-out inside a `%%metro direction: TB` section: one line continues straight down the trunk column to its child while a sibling peels off to another column. The continuation is slotted onto the trunk so it drops straight instead of jogging one offset step (#929).

Mermaid source

%%metro title: TB Trunk Through Fan
%%metro style: dark
%%metro line: a | A | #e63946
%%metro line: b | B | #0570b0

%%metro grid: work | 0,0

graph LR
    subgraph work [Work]
        %%metro direction: TB
        hub[Split]
        main[Main]
        sink[Collect]
        branch[Branch]
        hub -->|a| main
        main -->|a| sink
        hub -->|b| branch
    end

CLI command

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

Rendered map

Tb Passthrough Continuation

A TB convergence that is not a sink: a diagonal feeder continues straight down to a station directly below the merge while a collinear feeder peels off. The continuation rides the trunk slot so it drops straight, instead of being forced outboard where it kinks at the merge and crosses the collinear feeder (issue #1012).

Mermaid source

%%metro title: TB Passthrough Continuation
%%metro style: dark
%%metro line: r | R | #0570b0
%%metro line: g | G | #2db572
%%metro line: y | Y | #f5c542

%%metro grid: work | 0,0

graph LR
    subgraph work [Work]
        %%metro direction: TB
        starN[StarN]
        hisatN[HisatN]
        leftchild[LeftChild]
        merge[Merge]
        tail[Tail]
        starN -->|r| leftchild
        starN -->|g| merge
        hisatN -->|y| merge
        merge -->|g| tail
    end

CLI command

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

Rendered map

Tb Column Continuation Two Lines

A TB section with a two-line BOTTOM exit continuing straight down into the TB section below. The exit port seats close to the last station with normal section padding rather than the doubled gap the fold-span extension would add (issue #1062).

Mermaid source

%%metro title: TB Column Continuation Two Lines
%%metro style: dark
%%metro line: alpha | Alpha | #e63946
%%metro line: beta | Beta | #0570b0
%%metro grid: top_sec | 0,0
%%metro grid: bot_sec | 0,1

graph LR
    subgraph top_sec [Upper]
        %%metro direction: TB
        %%metro exit: bottom | alpha, beta
        t1[Refine]
        t2[Report]
        t1 -->|alpha,beta| t2
    end
    subgraph bot_sec [Lower]
        %%metro direction: TB
        %%metro entry: top | alpha, beta
        b1[Ingest]
        b2[Clean]
        b1 -->|alpha,beta| b2
    end
    t2 -->|alpha,beta| b1

CLI command

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

Rendered map

Tb Right Entry Stack

A two-line bundle into a stacked TB section's RIGHT entry from a same-row left source: it loops over the section top and descends into the port, the U-turn transposing the bundle, with concentric corners built via `build_concentric_bundle` (#707).

Mermaid source

%%metro title: TB Right-Entry Stack
%%metro style: dark
%%metro line: alpha | Alpha | #e63946
%%metro line: beta | Beta | #0570b0
%%metro grid: source | 0,0
%%metro grid: upper | 1,0
%%metro grid: lower | 1,1

graph LR
    subgraph source [Source]
        s1[Prepare A]
        s2[Prepare B]
        s1 -->|alpha| s2
    end

    subgraph upper [Upper]
        %%metro direction: TB
        %%metro entry: right | alpha, beta
        u1[Align]
        u2[Sort]
        u1 -->|alpha,beta| u2
    end

    subgraph lower [Lower]
        %%metro direction: TB
        %%metro entry: top | alpha, beta
        l1[Merge]
        l2[Report]
        l1 -->|alpha,beta| l2
    end

    s2 -->|alpha,beta| u1
    u2 -->|alpha,beta| l1

CLI command

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

Rendered map

Tb Bottom Entry Flow Start

A `%%metro direction: TB` section given `%%metro entry: bottom` whose consumer is the flow-start (top) station. The bottom entry is re-anchored to the top so the line enters beside its consumer and flows down, rather than running up through MultiQC to reach Collect and folding back (#885).

Mermaid source

%%metro title: TB Bottom Entry Flow Start
%%metro style: nfcore
%%metro line: reads | Reads | #1f77b4

graph LR
    subgraph up [Up]
        a[A]
        b[B]
        a -->|reads| b
    end
    subgraph qc [QC]
        %%metro direction: TB
        %%metro entry: bottom | reads
        collect[Collect]
        multiqc[MultiQC]
        collect -->|reads| multiqc
    end
    b -->|reads| collect

CLI command

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

Rendered map

Tb Left Exit Step

A TB alignment section exits LEFT into a lower right-entry section with a blocker directly below: the exit bundle steps west-down-west, routed as a parallel staircase that keeps the feed order (issue #671).

Mermaid source

%%metro title: TB left-exit staircase into a lower right-entry (issue #671)
%%metro line: a | Aligner A | #0570b0
%%metro line: b | Aligner B | #2db572
%%metro line: c | Aligner C | #f5c542
%%metro line: d | Side | #e63946
%%metro grid: src | 0,0
%%metro grid: align | 1,0
%%metro grid: blocker | 1,1
%%metro grid: post | 0,2

graph LR
    subgraph src [Source]
        ingest[Ingest]
    end
    subgraph align [Align]
        %%metro direction: TB
        hub[Hub]
        tail[Tail]
        hub -->|a,b,c| tail
    end
    subgraph blocker [Side]
        side[Side step]
    end
    subgraph post [Post]
        collect[Collect]
        report[Report]
        collect -->|a,b,c| report
    end

    ingest -->|a,b,c| hub
    ingest -->|d| side
    tail -->|a,b,c| collect

CLI command

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

Rendered map

Tb Lr Exit Left

A `%%metro direction: TB` section dropping in through its TOP entry and leaving through a LEFT exit into a section below-left (the `_route_tb_lr_exit` LEFT arm): the station drops, turns once, and runs out of the box's left side, the vertical leg fanned by the reversed station offset so the outermost line takes the widest arc (#917).

Mermaid source

%%metro title: TB Left Exit
%%metro style: dark
%%metro line: a | A | #e63946
%%metro line: b | B | #0570b0
%%metro grid: prep | 0,0
%%metro grid: work | 1,0
%%metro grid: report | 0,1

graph LR
    subgraph prep [Prep]
        p1[Start]
        p2[End]
        p1 -->|a,b| p2
    end
    subgraph work [Work]
        %%metro direction: TB
        %%metro entry: top | a,b
        %%metro exit: left | a,b
        w1[Process]
        w2[Collect]
        w1 -->|a,b| w2
    end
    subgraph report [Report]
        %%metro entry: right | a,b
        r1[Publish]
    end
    p2 -->|a,b| w1
    w2 -->|a,b| r1

CLI command

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

Rendered map

Tb Lr Exit Right

A `%%metro direction: TB` section dropping in through its TOP entry and leaving through a RIGHT exit into the next forward section (the `_route_tb_lr_exit` RIGHT arm): the mirror of the LEFT exit, fanned by the exit port's own offset (#917).

Mermaid source

%%metro title: TB Right Exit
%%metro style: dark
%%metro line: a | A | #e63946
%%metro line: b | B | #0570b0
%%metro grid: prep | 0,0
%%metro grid: work | 1,0
%%metro grid: report | 2,0

graph LR
    subgraph prep [Prep]
        p1[Start]
        p2[End]
        p1 -->|a,b| p2
    end
    subgraph work [Work]
        %%metro direction: TB
        %%metro entry: top | a,b
        %%metro exit: right | a,b
        w1[Process]
        w2[Collect]
        w1 -->|a,b| w2
    end
    subgraph report [Report]
        %%metro entry: left | a,b
        r1[Publish]
    end
    p2 -->|a,b| w1
    w2 -->|a,b| r1

CLI command

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

Rendered map

Tb Convergence Straight Drop

Two lines converge at a TB section's terminal merge; the feeder whose source is collinear with the merge drops dead straight while the sibling arrives diagonally, instead of the straight feeder kinking off its lane (issue #1007).

Mermaid source

%%metro title: TB Convergence Straight Drop
%%metro style: dark
%%metro line: a | A | #e63946
%%metro line: b | B | #0570b0

%%metro grid: work | 0,0

graph LR
    subgraph work [Work]
        %%metro direction: TB
        top[Top]
        side[Side]
        merge[Merge]
        top -->|a| merge
        side -->|b| merge
    end

CLI command

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

Rendered map

Tb Bottom Exit Fork Diamond

A TB section's BOTTOM exit forks to two stacked TB sections in different rows, the lower also fed by the upper (a diamond). The fork junction's leg into the nearer TOP entry drops straight in its column rather than jogging sideways and reversing at the boundary, and the leg continuing to the far section rides the intervening section's own trunk for the shared line as one stroke (issue #1058).

Mermaid source

%%metro line: alpha | Alpha | #e63946
%%metro grid: source | 0,0
%%metro grid: feed | 1,0
%%metro grid: mid | 1,1
%%metro grid: sink | 1,2

graph LR
    subgraph source [Source]
        s1[Start]
    end
    subgraph feed [Feed]
        %%metro direction: TB
        %%metro entry: right | alpha
        %%metro exit: bottom | alpha
        f1[Align]
        f2[Sort]
        f1 -->|alpha| f2
    end
    subgraph mid [Mid]
        %%metro direction: TB
        %%metro entry: top | alpha
        m1[Filter]
        m2[Classify]
        m1 -->|alpha| m2
    end
    subgraph sink [Sink]
        %%metro direction: TB
        %%metro entry: top | alpha
        sk1[Merge]
        sk2[Report]
        sk1 -->|alpha| sk2
    end
    s1 -->|alpha| f1
    f2 -->|alpha| m1
    f2 -->|alpha| sk1
    m2 -->|alpha| sk1

CLI command

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

Rendered map

Tb Bottom Exit Bundle Jog

A four-line bundle leaves a TB section's BOTTOM exit and jogs down into the TOP entry of an RL section placed in the row below and one column to the left. The four lines keep distinct channels through the jog instead of collapsing onto one (issue #1074).

Mermaid source

%%metro title: TB bottom-exit jog multi-line
%%metro line: l1 | L1 | #e6194b
%%metro line: l2 | L2 | #3cb44b
%%metro line: l3 | L3 | #4363d8
%%metro line: l4 | L4 | #f58231
%%metro grid: up | 1,0
%%metro grid: down | 0,1

graph TB
    subgraph up [Up]
        %%metro direction: TB
        %%metro entry: top | l1, l2, l3, l4
        %%metro exit: bottom | l1, l2, l3, l4
        a[A]
        b[B]
        a -->|l1,l2,l3,l4| b
    end
    subgraph down [Down]
        %%metro direction: RL
        %%metro entry: top | l1, l2, l3, l4
        cc[QC reporting node]
        dd[D]
        ee[E]
        cc -->|l1,l2,l3,l4| dd
        dd -->|l1,l2,l3,l4| ee
    end
    b -->|l1,l2,l3,l4| cc

CLI command

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

Rendered map

Tb Perp Exit Side Neighbour

A vertical-flow section's BOTTOM exit feeds a side LR neighbour sharing the exit's Y. The connector leaves the port down into the inter-row corridor clear of the box, runs across, then turns up into the entry, rather than running straight along the section's bottom edge and out through the corner (#1052).

Mermaid source

%%metro title: TB perp-exit into a side LR neighbour
%%metro line: a | A | #e63946
%%metro grid: work | 0,0
%%metro grid: out_sec | 1,0
graph LR
    subgraph work [Work]
        %%metro direction: TB
        %%metro exit: bottom | a
        w1[Demux]
        w2[Merge]
        w1 -->|a| w2
    end
    subgraph out_sec [Output]
        %%metro direction: LR
        %%metro entry: left | a
        o1[Publish]
    end
    w2 -->|a| o1

CLI command

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

Rendered map

Tb Two Line Vert Seam

A vertical-flow section's RIGHT exit feeds another vertical-flow section's LEFT entry with a two-line bundle. The entry sits a station gap above the trunk head so both lines enter horizontally then drop straight onto their trunk lanes, rather than the staggered line slanting into the trunk for want of drop room (#1054).

Mermaid source

%%metro title: TB into TB, horizontal seam
%%metro line: a | A | #e63946
%%metro line: b | B | #0570b0
%%metro grid: up_sec | 0,0
%%metro grid: down_sec | 1,0
graph LR
    subgraph up_sec [Left]
        %%metro direction: TB
        %%metro exit: right | a,b
        u1[Collect]
        u2[Reduce]
        u1 -->|a,b| u2
    end
    subgraph down_sec [Right]
        %%metro direction: TB
        %%metro entry: left | a,b
        d1[Split]
        d2[Emit]
        d1 -->|a,b| d2
    end
    u2 -->|a,b| d1

CLI command

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

Rendered map

Top Entry Header Clash

A TB section's title is long enough to reach under the trunk that drops into its TOP entry. Rather than route the line around the title, the header relocates below the box so the drop enters cleanly.

Mermaid source

%%metro title: Top Entry Header Clash
%%metro style: dark
%%metro line: a | A | #e63946

%%metro grid: src_sec | 0,0
%%metro grid: tgt_sec | 0,1

graph LR
    subgraph src_sec [Read QC]
        %%metro direction: LR
        s1[Trim]
        s2[Filter]
        s1 -->|a| s2
    end

    subgraph tgt_sec [Alignment and Sorting]
        %%metro direction: TB
        %%metro entry: top | a
        %%metro exit: right | a
        t1[Map Reads]
        t2[Sort BAM]
        t1 -->|a| t2
    end

    s2 -->|a| t1

CLI command

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

Rendered map

Header Side Rotated

A TB section whose trunk drops through the top edge and exits the bottom edge blocks the header on both horizontal edges. The title rotates and runs down the clear left edge instead of crossing the line.

Mermaid source

%%metro title: Header Rotated Onto Side
%%metro style: dark
%%metro line: a | A | #e63946

%%metro grid: src_sec | 0,0
%%metro grid: tgt_sec | 0,1
%%metro grid: snk_sec | 0,2

graph LR
    subgraph src_sec [Up]
        %%metro direction: TB
        %%metro exit: bottom | a
        s1[One]
    end

    subgraph tgt_sec [Align]
        %%metro direction: TB
        %%metro entry: top | a
        %%metro exit: bottom | a
        t1[Two]
        t2[Three]
        t1 -->|a| t2
    end

    subgraph snk_sec [Down]
        %%metro direction: TB
        %%metro entry: top | a
        k1[Four]
    end

    s1 -->|a| t1
    t2 -->|a| k1

CLI command

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

Rendered map

Header Nudge

A title too long to fit a rotated side, on a section blocked top and bottom by its trunk: the header shifts right past the trunk as a last resort, the canvas growing to keep it visible.

Mermaid source

%%metro title: Header Nudged Past Trunk
%%metro style: dark
%%metro line: a | A | #e63946

%%metro grid: src_sec | 0,0
%%metro grid: tgt_sec | 0,1
%%metro grid: snk_sec | 0,2

graph LR
    subgraph src_sec [Up]
        %%metro direction: TB
        %%metro exit: bottom | a
        s1[One]
    end

    subgraph tgt_sec [Alignment Sorting Markdup Stage]
        %%metro direction: TB
        %%metro entry: top | a
        %%metro exit: bottom | a
        t1[Two]
        t2[Three]
        t1 -->|a| t2
    end

    subgraph snk_sec [Down]
        %%metro direction: TB
        %%metro entry: top | a
        k1[Four]
    end

    s1 -->|a| t1
    t2 -->|a| k1

CLI command

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

Rendered map

Lr To Tb Top Drop

An LR section feeds the TOP entry of a TB section stacked directly below. With no explicit exit side the engine infers a BOTTOM exit: the line curves out of the trunk after the last station and drops straight onto the target trunk, which is aligned under the exit.

Mermaid source

%%metro title: LR to TB Top Drop
%%metro style: dark
%%metro line: a | A | #e63946

%%metro grid: src_sec | 0,0
%%metro grid: tgt_sec | 0,1

graph LR
    subgraph src_sec [Source]
        %%metro direction: LR
        s1[Start]
        s2[End]
        s1 -->|a| s2
    end

    subgraph tgt_sec [Target]
        %%metro direction: TB
        %%metro entry: top | a
        %%metro exit: right | a
        t1[Process]
        t2[Result]
        t1 -->|a| t2
    end

    s2 -->|a| t1

CLI command

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

Rendered map

Lr To Tb Top Drop Two Lines

Two co-travelling lines drop out of an LR section's explicit BOTTOM exit into a TB section's shared TOP entry below, staying parallel through the corner and down to the trunk without crossing.

Mermaid source

%%metro title: LR to TB Top Drop Two Lines
%%metro style: dark
%%metro line: a | A | #e63946
%%metro line: b | B | #0570b0

%%metro grid: src_sec | 0,0
%%metro grid: tgt_sec | 0,1

graph LR
    subgraph src_sec [Source]
        %%metro direction: LR
        %%metro exit: bottom | a,b
        s1[Start]
        s2[End]
        s1 -->|a,b| s2
    end

    subgraph tgt_sec [Target]
        %%metro direction: TB
        %%metro entry: top | a,b
        %%metro exit: right | a,b
        t1[Process]
        t2[Result]
        t1 -->|a,b| t2
    end

    s2 -->|a,b| t1

CLI command

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

Rendered map

Lr To Tb Top Near Vertical

A RIGHT-exit LR section feeds the TOP entry of a TB section stacked directly below. The explicit right exit leaves on the right, clears the source box, and doubles back over the inter-row gap to drop straight onto the target trunk rather than elbowing in through the top-right corner.

Mermaid source

%%metro title: Top Entry Near Vertical TB
%%metro style: dark
%%metro line: a | A | #e63946

%%metro grid: src_sec | 0,0
%%metro grid: tgt_sec | 0,1

graph LR
    subgraph src_sec [Source]
        %%metro direction: LR
        %%metro exit: right | a
        s1[Start]
        s2[End]
        s1 -->|a| s2
    end

    subgraph tgt_sec [Target]
        %%metro direction: TB
        %%metro entry: top | a
        %%metro exit: right | a
        t1[Process]
        t2[Result]
        t1 -->|a| t2
    end

    s2 -->|a| t1

CLI command

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

Rendered map

Lr To Tb Top Cross Col

A junction source feeds both a same-row RIGHT-entry consumer and a TB section's TOP entry two rows below. The downward branch drops onto the target trunk without crossing the section boundary off-port.

Mermaid source

%%metro title: Top Entry Horizontal Source
%%metro style: dark
%%metro line: a | A | #e63946
%%metro grid: src_sec | 0,0
%%metro grid: mid_sec | 1,0
%%metro grid: tgt_sec | 0,2
graph LR
    subgraph src_sec [Source]
        %%metro direction: LR
        %%metro exit: right | a
        s1[Start]
        s2[End]
        s1 -->|a| s2
    end
    subgraph mid_sec [Middle]
        %%metro direction: LR
        %%metro entry: left | a
        %%metro exit: right | a
        m1[Middle]
        m2[Middle Out]
        m1 -->|a| m2
    end
    subgraph tgt_sec [Target]
        %%metro direction: TB
        %%metro entry: top | a
        %%metro exit: right | a
        t1[Process]
        t2[Result]
        t1 -->|a| t2
    end
    s2 -->|a| m1
    s2 -->|a| t1

CLI command

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

Rendered map

Lr To Tb Top Two Lines

Two co-travelling lines from a RIGHT-exit LR section double back into a TB section's shared TOP entry below, landing on their trunk X offsets so the bundle stays parallel through the boundary without pinching or crossing.

Mermaid source

%%metro title: LR to TB Top Two Lines
%%metro style: dark
%%metro line: a | A | #e63946
%%metro line: b | B | #0570b0
%%metro grid: src_sec | 0,0
%%metro grid: tgt_sec | 0,1
graph LR
    subgraph src_sec [Source]
        %%metro direction: LR
        %%metro exit: right | a,b
        s1[Start]
        s2[End]
        s1 -->|a,b| s2
    end
    subgraph tgt_sec [Target]
        %%metro direction: TB
        %%metro entry: top | a,b
        %%metro exit: right | a,b
        t1[Process]
        t2[Result]
        t1 -->|a,b| t2
    end
    s2 -->|a,b| t1

CLI command

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

Rendered map

Serpentine Layout

Fold Fan Across

Three lines diverge, converge at a fold, then continue on the return row.

Mermaid source

%%metro title: Proteomics Quantification Pipeline
%%metro style: dark
%%metro line: tmt | TMT Labeling | #e63946
%%metro line: lfq | Label-Free | #457b9d
%%metro line: dia | DIA | #2a9d8f

graph LR
    subgraph sample_prep [Sample Preparation]
        sp_input[Input]
        sp_validate[Validate]
        sp_extract[Extract]
        sp_tag[Tag]
        sp_filt_a[Filter A]
        sp_filt_b[Filter B]
        sp_merge[Merge]
        sp_filter[QC Filter]
        sp_qc[Final QC]

        sp_input -->|tmt,lfq,dia| sp_validate
        sp_validate -->|tmt,lfq,dia| sp_extract
        sp_extract -->|tmt,lfq,dia| sp_tag
        sp_tag -->|tmt,lfq,dia| sp_filt_a
        sp_tag -->|tmt,lfq,dia| sp_filt_b
        sp_filt_a -->|tmt,lfq,dia| sp_merge
        sp_filt_b -->|tmt,lfq,dia| sp_merge
        sp_merge -->|tmt,lfq,dia| sp_filter
        sp_filter -->|tmt,lfq,dia| sp_qc
    end

    subgraph tmt_quant [TMT Quantification]
        tmt_label[Label]
        tmt_frac[Fractionate]
        tmt_pool[Pool]
        tmt_quant_ms[Quantify]
        tmt_check[Check]

        tmt_label -->|tmt| tmt_frac
        tmt_frac -->|tmt| tmt_pool
        tmt_pool -->|tmt| tmt_quant_ms
        tmt_quant_ms -->|tmt| tmt_check
    end

    subgraph lfq_quant [Label-Free Quantification]
        lfq_align[Align]
        lfq_quant_ms[Quantify]
        lfq_norm[Normalize]

        lfq_align -->|lfq| lfq_quant_ms
        lfq_quant_ms -->|lfq| lfq_norm
    end

    subgraph dia_quant [DIA Quantification]
        dia_window[Window]
        dia_extract[Extract]
        dia_quant_ms[Quantify]

        dia_window -->|dia| dia_extract
        dia_extract -->|dia| dia_quant_ms
    end

    subgraph normalize [Normalization]
        norm_input[Input]
        norm_calc[Calculate]
        norm_apply[Apply]

        norm_input -->|tmt,lfq,dia| norm_calc
        norm_calc -->|tmt,lfq,dia| norm_apply
    end

    subgraph stat_analysis [Statistical Analysis]
        stat_merge[Merge]
        diff_expr[Diff. Expression]
        pathway[Pathway]
        volcano[Volcano Plot]

        stat_merge -->|tmt,lfq,dia| diff_expr
        diff_expr -->|tmt,lfq,dia| pathway
        pathway -->|tmt,lfq,dia| volcano
    end

    subgraph reporting [Reporting]
        report_agg[Aggregate]
        report_mqc[MultiQC]
        report_final[Report]

        report_agg -->|tmt,lfq,dia| report_mqc
        report_mqc -->|tmt,lfq,dia| report_final
    end

    sp_qc -->|tmt| tmt_label
    sp_qc -->|lfq| lfq_align
    sp_qc -->|dia| dia_window
    tmt_check -->|tmt| norm_input
    lfq_norm -->|lfq| norm_input
    dia_quant_ms -->|dia| norm_input
    norm_apply -->|tmt,lfq,dia| stat_merge
    volcano -->|tmt,lfq,dia| report_agg

CLI command

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

Rendered map

Fold Left Exit Right Entry

A folded TB section's LEFT exit runs straight west into a relocated section's RIGHT entry. Regression fixture: the two joined sections share a bbox bottom so the straight run clears both edges by the same distance.

Mermaid source

%%metro title: Fold Left Exit Right Entry
%%metro style: dark
%%metro line: a | Line A | #2db572
%%metro line: b | Line B | #e6550d
%%metro line: c | Line C | #756bb1
%%metro fold_threshold: 4

graph LR
    subgraph inputs [Inputs]
        A_IN[ ]
        a1([A Step 1])
        a2([A Step 2])
        a3([A Step 3])
        B_IN[ ]
        C_IN[ ]
        A_IN -->|a| a1
        a1 -->|a| a2
        a2 -->|a| a3
    end

    subgraph middle [Middle]
        split([Split])
        prepare([Prepare])
        pred_x([Predict X])
        pred_y([Predict Y])
        pred_z([Predict Z])
        merge([Merge])
        split -->|a,b,c| prepare
        prepare -->|a,b,c| pred_x
        prepare -->|a,b,c| pred_y
        prepare -->|a,b,c| pred_z
        pred_x -->|a,b,c| merge
        pred_y -->|a,b,c| merge
        pred_z -->|a,b,c| merge
    end

    subgraph report [Report]
        summarize([Summarize])
        tsv_pad[ ]
        format([Format])
        TSV_OUT[ ]
        HTML_OUT[ ]
        summarize -->|a,b,c| tsv_pad
        summarize -->|a,b,c| format
        tsv_pad -->|a,b,c| TSV_OUT
        format -->|a,b,c| HTML_OUT
    end

    a3 -->|a| split
    B_IN -->|b| split
    C_IN -->|c| split
    merge -->|a,b,c| summarize

CLI command

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

Rendered map

Fold Double

Ten-section linear pipeline with two fold points (serpentine layout).

Mermaid source

%%metro title: WGS/WES Variant Pipeline
%%metro style: dark
%%metro line: wgs | Whole Genome | #2db572
%%metro line: wes | Whole Exome | #0570b0

graph LR
    subgraph input_qc [Input & QC]
        iq_input[Input]
        iq_fastqc[FastQC]
        iq_trim[Trim]
        iq_filter[Filter]

        iq_input -->|wgs,wes| iq_fastqc
        iq_fastqc -->|wgs,wes| iq_trim
        iq_trim -->|wgs,wes| iq_filter
    end

    subgraph alignment [Alignment]
        al_bwa[BWA-MEM2]
        al_sort[Sort]
        al_dedup[Dedup]
        al_bqsr[BQSR]

        al_bwa -->|wgs,wes| al_sort
        al_sort -->|wgs,wes| al_dedup
        al_dedup -->|wgs,wes| al_bqsr
    end

    subgraph base_recal [Base Recalibration]
        br_recal[Recalibrate]
        br_apply[Apply]
        br_validate[Validate]
        br_index[Index]

        br_recal -->|wgs,wes| br_apply
        br_apply -->|wgs,wes| br_validate
        br_validate -->|wgs,wes| br_index
    end

    subgraph calling [Variant Calling]
        vc_hc[HaplotypeCaller]
        vc_genotype[Genotype]
        vc_merge[Merge VCF]
        vc_norm[Normalize]

        vc_hc -->|wgs,wes| vc_genotype
        vc_genotype -->|wgs,wes| vc_merge
        vc_merge -->|wgs,wes| vc_norm
    end

    subgraph hard_filter [Hard Filtering]
        hf_sel_snp[Select SNPs]
        hf_sel_indel[Select Indels]
        hf_filt_snp[Filter SNPs]
        hf_filt_indel[Filter Indels]

        hf_sel_snp -->|wgs,wes| hf_filt_snp
        hf_filt_snp -->|wgs,wes| hf_sel_indel
        hf_sel_indel -->|wgs,wes| hf_filt_indel
    end

    subgraph annotation [Annotation]
        an_vep[VEP]
        an_snpsift[SnpSift]
        an_classify[Classify]
        an_prioritize[Prioritize]

        an_vep -->|wgs,wes| an_snpsift
        an_snpsift -->|wgs,wes| an_classify
        an_classify -->|wgs,wes| an_prioritize
    end

    subgraph interpretation [Interpretation]
        ip_pathogenicity[Pathogenicity]
        ip_frequency[Frequency]
        ip_clinical[Clinical]
        ip_aggregate[Aggregate]

        ip_pathogenicity -->|wgs,wes| ip_frequency
        ip_frequency -->|wgs,wes| ip_clinical
        ip_clinical -->|wgs,wes| ip_aggregate
    end

    subgraph integration [Integration]
        ig_merge[Merge Calls]
        ig_validate[Validate]
        ig_qc[QC Check]
        ig_finalize[Finalize]

        ig_merge -->|wgs,wes| ig_validate
        ig_validate -->|wgs,wes| ig_qc
        ig_qc -->|wgs,wes| ig_finalize
    end

    subgraph reporting [Reporting]
        rp_summary[Summary]
        rp_multiqc[MultiQC]
        rp_report[Report]

        rp_summary -->|wgs,wes| rp_multiqc
        rp_multiqc -->|wgs,wes| rp_report
    end

    subgraph archival [Archival]
        ar_archive[Archive]
        ar_compress[Compress]

        ar_archive -->|wgs,wes| ar_compress
    end

    iq_filter -->|wgs,wes| al_bwa
    al_bqsr -->|wgs,wes| br_recal
    br_index -->|wgs,wes| vc_hc
    vc_norm -->|wgs,wes| hf_sel_snp
    hf_filt_indel -->|wgs,wes| an_vep
    an_prioritize -->|wgs,wes| ip_pathogenicity
    ip_aggregate -->|wgs,wes| ig_merge
    ig_finalize -->|wgs,wes| rp_summary
    rp_report -->|wgs,wes| ar_archive

CLI command

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

Rendered map

Fold Stacked Branch

Stacked analysis sections feeding through a fold into branching targets.

Mermaid source

%%metro title: Single-Cell Multi-Omics Pipeline
%%metro style: dark
%%metro line: rna | scRNA-seq | #e63946
%%metro line: atac | scATAC-seq | #457b9d
%%metro line: protein | CITE-seq | #f5c542

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/fold_stacked_branch.mmd -o fold_stacked_branch.svg

Rendered map

Reconverge Reversed Fold

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

Mermaid source

%%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

Convergence Sink Fold

Convergence sink folded below its branches: a `fold_threshold` stacks the parallel branches in one column and drops the shared sink onto a lower row, fed through a TOP entry. Each upper branch's bottom-exit feeder routes around the intervening branch boxes through the clear left-side gap rather than ploughing straight down through them.

Mermaid source

%%metro title: Convergence Sink Fold
%%metro style: dark
%%metro fold_threshold: 3
%%metro line: main | Main | #0570b0

graph LR
    subgraph src [Source]
        s1[Input]
        s2[Prepare]
        s1 -->|main| s2
    end
    subgraph branch_a [Branch A]
        a1[Step A1]
        a2[Step A2]
        a1 -->|main| a2
    end
    subgraph branch_b [Branch B]
        b1[Step B1]
        b2[Step B2]
        b1 -->|main| b2
    end
    subgraph branch_c [Branch C]
        c1[Step C1]
        c2[Step C2]
        c1 -->|main| c2
    end
    subgraph sink [Sink]
        m1[Merge]
        m2[Report]
        m1 -->|main| m2
    end
    s2 -->|main| a1
    s2 -->|main| b1
    s2 -->|main| c1
    a2 -->|main| m1
    b2 -->|main| m1
    c2 -->|main| m1

CLI command

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

Rendered map

Riboseq Fold Two Dir Entry Hintless

A folded Ribo-seq excerpt with no `%%metro grid:`/`entry:`/`exit:` hints: P-site identification sits on the RL return row, fed from the quantification section directly above it and the ORF-calling section to its right. Entry-side inference picks a single sensible side (the flow-natural RIGHT, which a feed reaches) from the feed geometry, so the map lays out cleanly hint-free.

Mermaid source

%%metro title: Riboseq Fold Two-Direction Entry (hintless)
%%metro fold_threshold: 3
%%metro line: ribo | Ribo-seq | #2db572

graph LR
    subgraph prep [Prep]
        p0[Trim]
    end
    subgraph align [Align]
        a0[Align]
    end
    subgraph quantification [Quant]
        q0[Quantify]
    end
    subgraph orf_calling [ORF]
        o0[Call ORFs]
    end
    subgraph psite_id [P-site]
        ps0[P-sites]
    end
    subgraph te [TE]
        t0[TE]
    end
    p0 -->|ribo| a0
    a0 -->|ribo| q0
    q0 -->|ribo| o0
    q0 -->|ribo| ps0
    o0 -->|ribo| ps0
    ps0 -->|ribo| t0

CLI command

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

Rendered map

Riboseq Fold Two Dir Entry

The same folded Ribo-seq excerpt pinned with explicit grid cells and the hand-tuned `entry: top` incantation. Regression fixture for #1341's route-around and overlap goals: the top-declared entry drags the right-arriving feed and the P-site box overlaps its ORF neighbour. Compare the hint-free variant, which lays out cleanly.

Mermaid source

%%metro title: Riboseq Fold Two-Direction Entry
%%metro directional: true
%%metro line: ribo | Ribo-seq | #2db572
%%metro grid: prep | 0,0
%%metro grid: align | 1,0
%%metro grid: quantification | 2,0
%%metro grid: orf_calling | 3,1
%%metro grid: psite_id | 2,1
%%metro grid: te | 1,1

graph LR
    subgraph prep [Prep]
        p0[Trim]
    end
    subgraph align [Align]
        a0[Align]
    end
    subgraph quantification [Quant]
        q0[Quantify]
    end
    subgraph orf_calling [ORF]
        %%metro exit: left | ribo
        o0[Call ORFs]
    end
    subgraph psite_id [P-site]
        %%metro entry: top | ribo
        %%metro exit: left | ribo
        ps0[P-sites]
    end
    subgraph te [TE]
        %%metro entry: right | ribo
        t0[TE]
    end
    p0 -->|ribo| a0
    a0 -->|ribo| q0
    q0 -->|ribo| o0
    q0 -->|ribo| ps0
    o0 -->|ribo| ps0
    ps0 -->|ribo| t0

CLI command

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

Rendered map

Convergence Fold Diamond

Two distinct lines converging into a sink folded below its branches: a `fold_threshold` stacks both branches in one column and drops the shared sink onto a lower row, fed through a TOP entry. The two feeders, and the run through the merge, ride parallel approach channels rather than collapsing onto one vertical channel.

Mermaid source

%%metro title: Convergence Fold Diamond
%%metro style: dark
%%metro line: left_path | Left Path | #e63946
%%metro line: right_path | Right Path | #0570b0
%%metro fold_threshold: 4

graph LR
    subgraph start [Start]
        input[Input]
        prep[Prepare]
        input -->|left_path,right_path| prep
    end

    subgraph branch_left [Branch Left]
        l1[Left Step 1]
        l2[Left Step 2]
        l3[Left Step 3]
        l1 -->|left_path| l2
        l2 -->|left_path| l3
    end

    subgraph branch_right [Branch Right]
        r1[Right Step 1]
        r2[Right Step 2]
        r1 -->|right_path| r2
    end

    subgraph finish [Finish]
        merge[Merge]
        report[Report]
        merge -->|left_path,right_path| report
    end

    prep -->|left_path| l1
    prep -->|right_path| r1
    l3 -->|left_path| merge
    r2 -->|right_path| merge

CLI command

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

Rendered map

Fold Split Targets

Two folded branches dropping into one section through a shared TOP entry, each line continuing to its own separate sink (a fan, not a merge). The distinct-line drops stay collapsed onto the column trunk, since they part to different stations rather than bundling along a shared run.

Mermaid source

%%metro title: Fold Split Targets
%%metro style: dark
%%metro line: left_path | Left Path | #e63946
%%metro line: right_path | Right Path | #0570b0
%%metro fold_threshold: 4

graph LR
    subgraph start [Start]
        input[Input]
        prep[Prepare]
        input -->|left_path,right_path| prep
    end

    subgraph branch_left [Branch Left]
        l1[Left Step 1]
        l2[Left Step 2]
        l3[Left Step 3]
        l1 -->|left_path| l2
        l2 -->|left_path| l3
    end

    subgraph branch_right [Branch Right]
        r1[Right Step 1]
        r2[Right Step 2]
        r1 -->|right_path| r2
    end

    subgraph finish [Finish]
        recv_l[Recv Left]
        recv_r[Recv Right]
        out[Output]
        recv_l -->|left_path| out
        recv_r -->|right_path| out
    end

    prep -->|left_path| l1
    prep -->|right_path| r1
    l3 -->|left_path| recv_l
    r2 -->|right_path| recv_r

CLI command

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

Rendered map

Stacked Lr Serpentine

Same-direction sections stacked in one grid column, chained via short vertical drops on alternating sides (serpentine), no wrap-around.

Mermaid source

%%metro title: Stacked LR Serpentine
%%metro style: dark
%%metro line: main | Main | #e63946
%%metro grid: ingest | 0,0,3,1
%%metro grid: align | 1,0,1,1
%%metro grid: dedup | 1,1,1,1
%%metro grid: call | 1,2,1,1

graph LR
    subgraph ingest [Ingest]
        i1[Read]
        i2[QC]
        i1 -->|main| i2
    end

    subgraph align [Alignment]
        a1[Map]
        a2[Sort]
        a1 -->|main| a2
    end

    subgraph dedup [Dedup]
        d1[Mark Dup]
        d2[Recalibrate]
        d1 -->|main| d2
    end

    subgraph call [Variant Calling]
        c1[Call]
        c2[Filter]
        c1 -->|main| c2
    end

    i2 -->|main| a1
    a2 -->|main| d1
    d2 -->|main| c1

CLI command

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

Rendered map

Serpentine Grid Wide Bundle

A two-line bundle folds through a 3x2 section grid: each row flows left to right, and the bundle wraps from the right of one row to the left of the next. The wrap spans more than one column, so its return run loops through the clear inter-row gap with both lines kept fanned around every corner.

Mermaid source

%%metro title: Serpentine Grid Wide Bundle
%%metro style: dark
%%metro line: a | Line A | #4a90d9
%%metro line: b | Line B | #e63946
%%metro grid: s1 | 0,0
%%metro grid: s2 | 1,0
%%metro grid: s3 | 2,0
%%metro grid: s4 | 0,1
%%metro grid: s5 | 1,1
%%metro grid: s6 | 2,1

graph LR
    subgraph s1 [Sec 1]
        %%metro exit: right | a, b
        n1[Alpha]
        n2[Beta]
        n1 -->|a,b| n2
    end
    subgraph s2 [Sec 2]
        %%metro entry: left | a, b
        %%metro exit: right | a, b
        n3[Gamma]
        n4[Delta]
        n3 -->|a,b| n4
    end
    subgraph s3 [Sec 3]
        %%metro entry: left | a, b
        %%metro exit: right | a, b
        n5[Epsilon]
        n6[Zeta]
        n5 -->|a,b| n6
    end
    subgraph s4 [Sec 4]
        %%metro entry: left | a, b
        %%metro exit: right | a, b
        n7[Eta]
        n8[Theta]
        n7 -->|a,b| n8
    end
    subgraph s5 [Sec 5]
        %%metro entry: left | a, b
        %%metro exit: right | a, b
        n9[Iota]
        n10[Kappa]
        n9 -->|a,b| n10
    end
    subgraph s6 [Sec 6]
        %%metro entry: left | a, b
        n11[Lambda]
        n12[Mu]
        n11 -->|a,b| n12
    end
    n2 -->|a,b| n3
    n4 -->|a,b| n5
    n6 -->|a,b| n7
    n8 -->|a,b| n9
    n10 -->|a,b| n11

CLI command

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

Rendered map

Serpentine Grid Tall Bundle

A two-line bundle folds through a 2x3 section grid, wrapping twice. Each wrap returns through its own inter-row gap, so the two stacked return runs stay on distinct channels rather than collapsing onto one.

Mermaid source

%%metro title: Serpentine Grid Tall Bundle
%%metro style: dark
%%metro line: a | Line A | #4a90d9
%%metro line: b | Line B | #e63946
%%metro grid: s1 | 0,0
%%metro grid: s2 | 1,0
%%metro grid: s3 | 0,1
%%metro grid: s4 | 1,1
%%metro grid: s5 | 0,2
%%metro grid: s6 | 1,2

graph LR
    subgraph s1 [Sec 1]
        %%metro exit: right | a, b
        n1[Alpha]
        n2[Beta]
        n1 -->|a,b| n2
    end
    subgraph s2 [Sec 2]
        %%metro entry: left | a, b
        %%metro exit: right | a, b
        n3[Gamma]
        n4[Delta]
        n3 -->|a,b| n4
    end
    subgraph s3 [Sec 3]
        %%metro entry: left | a, b
        %%metro exit: right | a, b
        n5[Epsilon]
        n6[Zeta]
        n5 -->|a,b| n6
    end
    subgraph s4 [Sec 4]
        %%metro entry: left | a, b
        %%metro exit: right | a, b
        n7[Eta]
        n8[Theta]
        n7 -->|a,b| n8
    end
    subgraph s5 [Sec 5]
        %%metro entry: left | a, b
        %%metro exit: right | a, b
        n9[Iota]
        n10[Kappa]
        n9 -->|a,b| n10
    end
    subgraph s6 [Sec 6]
        %%metro entry: left | a, b
        n11[Lambda]
        n12[Mu]
        n11 -->|a,b| n12
    end
    n2 -->|a,b| n3
    n4 -->|a,b| n5
    n6 -->|a,b| n7
    n8 -->|a,b| n9
    n10 -->|a,b| n11

CLI command

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

Rendered map

Serpentine Rl Bundle

A true boustrophedon fold of a two-line bundle: the top row flows left to right, drops straight down the right edge, and the return row flows right to left via direction: RL. The bundle stays on the outside of the fold the whole way round (top, right, then bottom) with no crossover, and the descent column aligns under the exit so the drop is a clean U.

Mermaid source

%%metro title: Serpentine RL Bundle
%%metro style: dark
%%metro line: dna | DNA | #4a90d9
%%metro line: rna | RNA | #e63946
%%metro grid: preprocessing | 0,0
%%metro grid: gatk | 1,0
%%metro grid: variant_calling | 2,0
%%metro grid: normalization | 2,1
%%metro grid: consensus | 1,1
%%metro grid: realignment | 0,1

graph LR
    subgraph preprocessing [Pre-processing]
        %%metro exit: right | dna, rna
        pp1[Trim]
        pp2[Align]
        pp1 -->|dna,rna| pp2
    end
    subgraph gatk [GATK]
        %%metro entry: left | dna, rna
        %%metro exit: right | dna, rna
        gk1[BQSR]
        gk2[Apply]
        gk1 -->|dna,rna| gk2
    end
    subgraph variant_calling [Variant Calling]
        %%metro entry: left | dna, rna
        %%metro exit: bottom | dna, rna
        vc1[Call]
        vc2[Filter]
        vc1 -->|dna,rna| vc2
    end
    subgraph normalization [Normalization]
        %%metro direction: RL
        %%metro entry: top | dna, rna
        %%metro exit: left | dna, rna
        nz1[Decompose]
        nz2[Norm]
        nz1 -->|dna,rna| nz2
    end
    subgraph consensus [Consensus]
        %%metro direction: RL
        %%metro entry: right | dna, rna
        %%metro exit: left | dna, rna
        cs1[Merge]
        cs2[Vote]
        cs1 -->|dna,rna| cs2
    end
    subgraph realignment [Realignment]
        %%metro direction: RL
        %%metro entry: right | dna, rna
        rl1[Realign]
        rl2[Recall]
        rl1 -->|dna,rna| rl2
    end
    pp2 -->|dna,rna| gk1
    gk2 -->|dna,rna| vc1
    vc2 -->|dna,rna| nz1
    nz2 -->|dna,rna| cs1
    cs2 -->|dna,rna| rl1

CLI command

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

Rendered map

Lr Bottom Exit Rl Top Entry Jog

An LR section's bottom exit drops straight into the top entry of the direction: RL section stacked directly below it. The receiving RL section reserves an offset slot for a line that peels off inside it, so the descent inherits that wider anchoring and lands square on the entry port with no sideways jog at the boundary (issue #1212).

Mermaid source

%%metro title: LR bottom-exit RL top-entry
%%metro style: dark
%%metro line: dna | DNA | #4a90d9
%%metro line: rna | RNA | #e63946
%%metro line: extra | Extra | #f5c542
%%metro grid: preprocessing | 0,0
%%metro grid: gatk | 1,0
%%metro grid: normalization | 2,0
%%metro grid: consensus | 2,1
%%metro grid: realign | 1,1
%%metro grid: reporting | 0,1

graph LR
    subgraph preprocessing [Pre-processing]
        pp1[Trim]
        pp2[Align]
        pp1 -->|dna,rna| pp2
    end
    subgraph gatk [GATK]
        gk1[BQSR]
        gk2[Apply]
        gk1 -->|dna,rna| gk2
    end
    subgraph normalization [Normalization]
        %%metro exit: bottom | dna, rna
        nz1[Decompose]
        nz2[Norm]
        nz3[Annot]
        nz1 -->|dna,rna| nz2
        nz2 -->|dna,rna| nz3
    end
    subgraph consensus [Consensus]
        %%metro direction: RL
        %%metro entry: top | dna, rna
        cs1[vcf2MAF]
        cs2[Consensus]
        cs3[MAFFilter]
        cs1 -->|dna,rna| cs2
        cs2 -->|dna,rna| cs3
    end
    subgraph realign [Realignment]
        %%metro direction: RL
        re1[MAF2BED]
        re2[Extract]
        re3[Recall]
        re1 -->|extra| re2
        re2 -->|extra| re3
    end
    subgraph reporting [Reporting]
        %%metro direction: RL
        rp1[RNAFilter]
        rp2[MultiQC]
        rp1 -->|rna,extra| rp2
    end
    pp2 -->|dna,rna| gk1
    gk2 -->|dna,rna| nz1
    nz3 -->|dna,rna| cs1
    cs3 -->|extra| re1
    cs3 -->|rna| rp1
    re3 -->|extra| rp1

CLI command

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

Rendered map

Manual Rl Row Nonconsumer Bypass

A manual-grid serpentine whose return row flows right to left via direction: RL. A non-consumer line shares an exit bundle with a consumed line but is not consumed by the intervening RL section, so it must bypass around that section rather than route through its interior. The descent column lands in the clear gap beside the intervening box and the line loops below the whole row into its target (issue #1211).

Mermaid source

%%metro title: Manual RL row non-consumer bypass
%%metro style: nfcore
%%metro fold_threshold: 15
%%metro file: fastq_in | FASTQ
%%metro file: report_out | HTML
%%metro line: dna | DNA (Tumor + Normal) | #4a90d9
%%metro line: rna | RNA (Tumor) | #e63946
%%metro line: realignment | Realignment (RNA) | #f5c542
%%metro line_order: definition
%%metro legend: bl
%%metro grid: preprocessing | 0,0
%%metro grid: gatk_preproc | 1,0
%%metro grid: variant_calling | 2,0
%%metro grid: normalization | 3,0
%%metro grid: consensus | 3,1
%%metro grid: realign | 1,1,2,1
%%metro grid: reporting | 0,1

graph LR
    subgraph preprocessing [Pre-processing & Alignment]
        fastq_in[ ]
        fastqc[FastQC]
        fastp[fastp]
        bwa_mem[BWA-mem/BWA-mem2]
        star[STAR]
        samtools_merge[SAMtools Merge]

        fastq_in -->|dna,rna| fastqc
        fastqc -->|dna,rna| fastp
        fastp -->|dna| bwa_mem
        fastp -->|rna| star
        bwa_mem -->|dna| samtools_merge
        star -->|rna| samtools_merge
    end

    subgraph gatk_preproc [GATK Preprocessing]
        markduplicates[MarkDuplicates]
        splitncigar[SplitNCigarReads]
        baserecalibrator[BaseRecalibrator]
        applybqsr[ApplyBQSR]
        samtools_stats[SAMtools Stats]
        mosdepth[Mosdepth]

        markduplicates -->|dna| baserecalibrator
        markduplicates -->|rna| splitncigar
        splitncigar -->|rna| baserecalibrator
        baserecalibrator -->|dna,rna| applybqsr
        applybqsr -->|dna,rna| samtools_stats
        samtools_stats -->|dna,rna| mosdepth
    end

    subgraph variant_calling [Variant Calling (parallel)]
        vc_fork[ ]
        mutect2[Mutect2]
        strelka[Strelka2]
        sage[SAGE]
        vc_join[ ]

        vc_fork -->|dna,rna| mutect2
        vc_fork -->|dna,rna| strelka
        vc_fork -->|dna,rna| sage
        mutect2 -->|dna,rna| vc_join
        strelka -->|dna,rna| vc_join
        sage -->|dna,rna| vc_join
    end

    subgraph normalization [Normalization & Annotation]
        %%metro exit: bottom | dna, rna
        vt_decompose[VT Decompose]
        vt_normalize[VT Normalize]
        ensemblvep[Ensembl VEP]

        vt_decompose -->|dna,rna| vt_normalize
        vt_normalize -->|dna,rna| ensemblvep
    end

    subgraph consensus [Consensus & Filtering]
        %%metro direction: RL
        %%metro entry: top | dna, rna
        %%metro exit: left | rna, realignment
        vcf2maf[vcf2MAF]
        run_consensus[Consensus]
        maf_filtering[MAF Filtering]

        vcf2maf -->|dna,rna| run_consensus
        run_consensus -->|dna,rna| maf_filtering
    end

    subgraph realign [Realignment (RNA)]
        %%metro direction: RL
        %%metro entry: right | realignment
        %%metro exit: left | realignment
        maf2bed[MAF2BED]
        extract_reads[Extract Reads]
        hisat2[HISAT2]
        markdup_re[MarkDuplicates]
        splitncigar_re[SplitNCigarReads]
        bqsr_re[BQSR]
        varcall_re[Variant Calling]
        norm_re[Normalization]
        annotate_re[Annotation]
        consensus_re[Consensus]
        filter_re[MAF Filtering]

        maf2bed -->|realignment| extract_reads
        extract_reads -->|realignment| hisat2
        hisat2 -->|realignment| markdup_re
        markdup_re -->|realignment| splitncigar_re
        splitncigar_re -->|realignment| bqsr_re
        bqsr_re -->|realignment| varcall_re
        varcall_re -->|realignment| norm_re
        norm_re -->|realignment| annotate_re
        annotate_re -->|realignment| consensus_re
        consensus_re -->|realignment| filter_re
    end

    subgraph reporting [Reporting]
        %%metro direction: RL
        %%metro entry: right | rna, realignment
        rna_filter[RNA MAF Filtering]
        rna_filter -->|rna,realignment| multiqc
        multiqc[MultiQC]
        report_out[ ]

        multiqc -->|rna,realignment| report_out
    end

    %% Inter-section edges
    maf_filtering -->|realignment| maf2bed
    samtools_merge -->|dna,rna| markduplicates
    mosdepth -->|dna,rna| vc_fork
    vc_join -->|dna,rna| vt_decompose
    ensemblvep -->|dna,rna| vcf2maf
    filter_re -->|realignment| rna_filter
    maf_filtering -->|rna| rna_filter

CLI command

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

Rendered map

Packed Cell Cellmate Bypass

The same non-consumer bypass as manual_rl_row_nonconsumer_bypass, but the intervening section is packed into the same grid cell as the target rather than given its own cell. The bypass must still loop around the cell-mate's box instead of cutting straight through it (issue #1228).

Mermaid source

%%metro title: Packed-cell non-consumer bypass
%%metro style: nfcore
%%metro fold_threshold: 15
%%metro file: fastq_in | FASTQ
%%metro file: report_out | HTML
%%metro line: dna | DNA (Tumor + Normal) | #4a90d9
%%metro line: rna | RNA (Tumor) | #e63946
%%metro line: realignment | Realignment (RNA) | #f5c542
%%metro line_order: definition
%%metro legend: bl
%%metro grid: preprocessing | 0,0
%%metro grid: gatk_preproc | 1,0
%%metro grid: variant_calling | 2,0
%%metro grid: normalization | 3,0
%%metro grid: consensus | 3,1
%%metro grid: realign, reporting | 1,1

graph LR
    subgraph preprocessing [Pre-processing & Alignment]
        fastq_in[ ]
        fastqc[FastQC]
        fastp[fastp]
        bwa_mem[BWA-mem/BWA-mem2]
        star[STAR]
        samtools_merge[SAMtools Merge]

        fastq_in -->|dna,rna| fastqc
        fastqc -->|dna,rna| fastp
        fastp -->|dna| bwa_mem
        fastp -->|rna| star
        bwa_mem -->|dna| samtools_merge
        star -->|rna| samtools_merge
    end

    subgraph gatk_preproc [GATK Preprocessing]
        markduplicates[MarkDuplicates]
        splitncigar[SplitNCigarReads]
        baserecalibrator[BaseRecalibrator]
        applybqsr[ApplyBQSR]
        samtools_stats[SAMtools Stats]
        mosdepth[Mosdepth]

        markduplicates -->|dna| baserecalibrator
        markduplicates -->|rna| splitncigar
        splitncigar -->|rna| baserecalibrator
        baserecalibrator -->|dna,rna| applybqsr
        applybqsr -->|dna,rna| samtools_stats
        samtools_stats -->|dna,rna| mosdepth
    end

    subgraph variant_calling [Variant Calling (parallel)]
        vc_fork[ ]
        mutect2[Mutect2]
        strelka[Strelka2]
        sage[SAGE]
        vc_join[ ]

        vc_fork -->|dna,rna| mutect2
        vc_fork -->|dna,rna| strelka
        vc_fork -->|dna,rna| sage
        mutect2 -->|dna,rna| vc_join
        strelka -->|dna,rna| vc_join
        sage -->|dna,rna| vc_join
    end

    subgraph normalization [Normalization & Annotation]
        %%metro exit: bottom | dna, rna
        vt_decompose[VT Decompose]
        vt_normalize[VT Normalize]
        ensemblvep[Ensembl VEP]

        vt_decompose -->|dna,rna| vt_normalize
        vt_normalize -->|dna,rna| ensemblvep
    end

    subgraph consensus [Consensus & Filtering]
        %%metro direction: RL
        %%metro entry: top | dna, rna
        %%metro exit: left | rna, realignment
        vcf2maf[vcf2MAF]
        run_consensus[Consensus]
        maf_filtering[MAF Filtering]

        vcf2maf -->|dna,rna| run_consensus
        run_consensus -->|dna,rna| maf_filtering
    end

    subgraph realign [Realignment (RNA)]
        %%metro direction: RL
        %%metro entry: right | realignment
        %%metro exit: left | realignment
        maf2bed[MAF2BED]
        extract_reads[Extract Reads]
        hisat2[HISAT2]
        markdup_re[MarkDuplicates]
        splitncigar_re[SplitNCigarReads]
        bqsr_re[BQSR]
        varcall_re[Variant Calling]
        norm_re[Normalization]
        annotate_re[Annotation]
        consensus_re[Consensus]
        filter_re[MAF Filtering]

        maf2bed -->|realignment| extract_reads
        extract_reads -->|realignment| hisat2
        hisat2 -->|realignment| markdup_re
        markdup_re -->|realignment| splitncigar_re
        splitncigar_re -->|realignment| bqsr_re
        bqsr_re -->|realignment| varcall_re
        varcall_re -->|realignment| norm_re
        norm_re -->|realignment| annotate_re
        annotate_re -->|realignment| consensus_re
        consensus_re -->|realignment| filter_re
    end

    subgraph reporting [Reporting]
        %%metro direction: RL
        %%metro entry: right | rna, realignment
        rna_filter[RNA MAF Filtering]
        rna_filter -->|rna,realignment| multiqc
        multiqc[MultiQC]
        report_out[ ]

        multiqc -->|rna,realignment| report_out
    end

    %% Inter-section edges
    maf_filtering -->|realignment| maf2bed
    samtools_merge -->|dna,rna| markduplicates
    mosdepth -->|dna,rna| vc_fork
    vc_join -->|dna,rna| vt_decompose
    ensemblvep -->|dna,rna| vcf2maf
    filter_re -->|realignment| rna_filter
    maf_filtering -->|rna| rna_filter

CLI command

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

Rendered map

Packed Cell Cellmate Bypass Adjacent

The packed-cell cell-mate bypass with the bypassing line's source section sitting in the column immediately adjacent to the packed cell, with no gap column to descend through. The bypass must still loop below the cell-mate's box rather than collapse back to a straight run through its interior (issue #1233).

Mermaid source

%%metro title: Packed-cell non-consumer bypass (adjacent source)
%%metro style: nfcore
%%metro fold_threshold: 15
%%metro file: fastq_in | FASTQ
%%metro file: report_out | HTML
%%metro line: dna | DNA (Tumor + Normal) | #4a90d9
%%metro line: rna | RNA (Tumor) | #e63946
%%metro line: realignment | Realignment (RNA) | #f5c542
%%metro line_order: definition
%%metro legend: bl
%%metro grid: preprocessing | 0,0
%%metro grid: gatk_preproc, variant_calling | 1,0
%%metro grid: normalization | 2,0
%%metro grid: consensus | 2,1
%%metro grid: realign, reporting | 1,1

graph LR
    subgraph preprocessing [Pre-processing & Alignment]
        fastq_in[ ]
        fastqc[FastQC]
        fastp[fastp]
        bwa_mem[BWA-mem/BWA-mem2]
        star[STAR]
        samtools_merge[SAMtools Merge]

        fastq_in -->|dna,rna| fastqc
        fastqc -->|dna,rna| fastp
        fastp -->|dna| bwa_mem
        fastp -->|rna| star
        bwa_mem -->|dna| samtools_merge
        star -->|rna| samtools_merge
    end

    subgraph gatk_preproc [GATK Preprocessing]
        markduplicates[MarkDuplicates]
        splitncigar[SplitNCigarReads]
        baserecalibrator[BaseRecalibrator]
        applybqsr[ApplyBQSR]
        samtools_stats[SAMtools Stats]
        mosdepth[Mosdepth]

        markduplicates -->|dna| baserecalibrator
        markduplicates -->|rna| splitncigar
        splitncigar -->|rna| baserecalibrator
        baserecalibrator -->|dna,rna| applybqsr
        applybqsr -->|dna,rna| samtools_stats
        samtools_stats -->|dna,rna| mosdepth
    end

    subgraph variant_calling [Variant Calling (parallel)]
        vc_fork[ ]
        mutect2[Mutect2]
        strelka[Strelka2]
        sage[SAGE]
        vc_join[ ]

        vc_fork -->|dna,rna| mutect2
        vc_fork -->|dna,rna| strelka
        vc_fork -->|dna,rna| sage
        mutect2 -->|dna,rna| vc_join
        strelka -->|dna,rna| vc_join
        sage -->|dna,rna| vc_join
    end

    subgraph normalization [Normalization & Annotation]
        %%metro exit: bottom | dna, rna
        vt_decompose[VT Decompose]
        vt_normalize[VT Normalize]
        ensemblvep[Ensembl VEP]

        vt_decompose -->|dna,rna| vt_normalize
        vt_normalize -->|dna,rna| ensemblvep
    end

    subgraph consensus [Consensus & Filtering]
        %%metro direction: RL
        %%metro entry: top | dna, rna
        %%metro exit: left | rna, realignment
        vcf2maf[vcf2MAF]
        run_consensus[Consensus]
        maf_filtering[MAF Filtering]

        vcf2maf -->|dna,rna| run_consensus
        run_consensus -->|dna,rna| maf_filtering
    end

    subgraph realign [Realignment (RNA)]
        %%metro direction: RL
        %%metro entry: right | realignment
        %%metro exit: left | realignment
        maf2bed[MAF2BED]
        extract_reads[Extract Reads]
        hisat2[HISAT2]
        markdup_re[MarkDuplicates]
        splitncigar_re[SplitNCigarReads]
        bqsr_re[BQSR]
        varcall_re[Variant Calling]
        norm_re[Normalization]
        annotate_re[Annotation]
        consensus_re[Consensus]
        filter_re[MAF Filtering]

        maf2bed -->|realignment| extract_reads
        extract_reads -->|realignment| hisat2
        hisat2 -->|realignment| markdup_re
        markdup_re -->|realignment| splitncigar_re
        splitncigar_re -->|realignment| bqsr_re
        bqsr_re -->|realignment| varcall_re
        varcall_re -->|realignment| norm_re
        norm_re -->|realignment| annotate_re
        annotate_re -->|realignment| consensus_re
        consensus_re -->|realignment| filter_re
    end

    subgraph reporting [Reporting]
        %%metro direction: RL
        %%metro entry: right | rna, realignment
        rna_filter[RNA MAF Filtering]
        rna_filter -->|rna,realignment| multiqc
        multiqc[MultiQC]
        report_out[ ]

        multiqc -->|rna,realignment| report_out
    end

    %% Inter-section edges
    maf_filtering -->|realignment| maf2bed
    samtools_merge -->|dna,rna| markduplicates
    mosdepth -->|dna,rna| vc_fork
    vc_join -->|dna,rna| vt_decompose
    ensemblvep -->|dna,rna| vcf2maf
    filter_re -->|realignment| rna_filter
    maf_filtering -->|rna| rna_filter

CLI command

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

Rendered map

Branch Fold Forward

A side branch (Aux) shares a topo column with the spine (Genome). At a low fold threshold the serpentine packer skips that branch column as a fold point - folding it would strand Genome's consumer (Post) behind it - and folds the spine instead, so every inter-section edge flows forward and Genome's exit faces Post (issue #1080).

Mermaid source

%%metro title: Branch fold stays forward
%%metro fold_threshold: 6
%%metro line: main | Main | #0570b0
%%metro line: side | Side | #e63946

graph LR
    subgraph intake [Intake]
        i0[ ]
        i1[Trim]
        i2[Filter]
        i3[QC]
        i0 -->|main,side| i1
        i1 -->|main,side| i2
        i2 -->|main,side| i3
    end
    subgraph genome [Genome]
        %%metro entry: left | main
        %%metro exit: right | main
        g0[Align]
        g1[Dedup]
        g2[Quant]
        g0 -->|main| g1
        g1 -->|main| g2
    end
    subgraph aux [Aux]
        %%metro entry: left | side
        a0[Pseudo]
        a1[Count]
        a0 -->|side| a1
    end
    subgraph post [Post]
        %%metro entry: left | main
        %%metro exit: bottom | main
        p0[Mark]
        p1[Track]
        p0 -->|main| p1
    end
    subgraph report [Report]
        %%metro direction: RL
        %%metro entry: top | main
        r0[Collect]
        r1[ ]
        r0 -->|main| r1
    end
    i3 -->|main| g0
    i3 -->|side| a0
    g2 -->|main| p0
    p1 -->|main| r0

CLI command

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

Rendered map

Branch Fold Stability

A wide side branch (Survey) shares a topo column with the spine and sits one station below its fold threshold. Adding a station inside Survey must not re-grid the downstream Report onto a backward return row: inter-section placement is a function of the DAG, not of intra-section size (issue #1082).

Mermaid source

%%metro title: Branch-fold placement stability
%%metro style: dark
%%metro fold_threshold: 6
%%metro line: survey | Survey | #0570b0
%%metro line: align | Alignment | #2db572

graph LR
    subgraph ingest [Ingest]
        i1[Read]
        i2[Validate]
        i1 -->|survey,align| i2
    end

    subgraph survey [Survey]
        s1[Sketch]
        s2[Profile]
        s3[Classify]
        s4[Summarise]
        s1 -->|survey| s2
        s2 -->|survey| s3
        s3 -->|survey| s4
    end

    subgraph align [Alignment]
        a1[Index]
        a2[Map]
        a1 -->|align| a2
    end

    subgraph report [Report]
        r1[Aggregate]
        r2[Publish]
        r1 -->|align| r2
    end

    i2 -->|survey| s1
    i2 -->|align| a1
    a2 -->|align| r1

CLI command

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

Rendered map

Rl Entry Right Exit Left

A return-row section fed from the right that exits left, where the right entry feeds the section's internal flow-sink. The section resolves to RL flow rather than reading the declared ports as an in-place reversal (issue #1298).

Mermaid source

%%metro title: RL entry-right exit-left
%%metro line: a | A | #e6007e
%%metro grid: feed | 2,0
%%metro grid: mid | 1,0
%%metro grid: sink | 0,0

graph LR
    subgraph feed [Feed]
        %%metro exit: left | a
        f1[F1]
    end
    subgraph mid [Mid]
        %%metro entry: right | a
        %%metro exit: left | a
        m1[M1]
        m2[M2]
        m1 -->|a| m2
    end
    subgraph sink [Sink]
        %%metro entry: right | a
        s1[S1]
    end
    f1 -->|a| m2
    m2 -->|a| s1

CLI command

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

Rendered map

Inter-section Routing

Same Side Culdesac

A line declares its entry on a reversed (RL) section's flow-trailing edge, the edge the section flows out of, but its consumer is an interior station held off the leading end by a file terminus. Rather than fold the line back over the trunk to reach it, the entry re-anchors to the section's leading edge; the producer then reaches it by wrapping over the section top, so the line reads as a clean loop and the consumer is a straight pass-through.

Mermaid source

%%metro title: Same-Side Cul-de-Sac
%%metro style: dark
%%metro directional: true
%%metro line: flow | Flow | #0570b0
%%metro line: feed | Feed | #41ab5d
%%metro file: f | FASTQ
%%metro grid: producer | 0,0
%%metro grid: mid | 1,0

graph LR
    subgraph producer [Producer]
        p1[Source]
        p2[Prepare]
        p1 -->|flow| p2
    end
    subgraph mid [Cul-de-sac]
        %%metro direction: RL
        %%metro entry: left | flow
        f[ ]
        inner[Inner]
        outer[Outer]
        f -->|feed| inner
        inner -->|flow| outer
    end
    p2 -->|flow| inner

CLI command

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

Rendered map

Left Exit Sink Below

A TB bridge's LEFT exit feeds a LEFT-entry sink one row below and to the left: the bundle leads out left and drops straight down a channel clear of both boxes, routing around the bridge rather than clawing back through its interior (issue #1083).

Mermaid source

%%metro title: LEFT exit feeds a LEFT-entry sink one row below and to the left
%%metro line: main | Main | #e64980
%%metro grid: pre | 0,0
%%metro grid: align | 1,0
%%metro grid: bridge | 2,0
%%metro grid: sink | 1,1

graph LR
    subgraph pre [Pre]
        p1[P1] -->|main| p2[P2]
    end
    subgraph align [Align]
        a1[A1] -->|main| a2[A2]
    end
    subgraph bridge [Bridge]
        %%metro direction: TB
        %%metro entry: top | main
        %%metro exit: left | main
        b1[B1] -->|main| b2[B2]
        b2 -->|main| b3[B3]
        b3 -->|main| b4[B4]
    end
    subgraph sink [Sink]
        %%metro entry: left | main
        s1[S1] -->|main| s2[S2]
    end
    p2 -->|main| a1
    a2 -->|main| b1
    b4 -->|main| s1

CLI command

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

Rendered map

Right Entry Gap Above Empty Row

A right-entry feed from a source two rows above its target, where the target flows right-to-left so its flow-start consumer sits at the entry edge: the feed loops around below into the port beside the consumer rather than crossing the box and folding back (#885).

Mermaid source

%%metro title: Right Entry Gap Above Empty Row
%%metro style: dark
%%metro line: a | A | #e63946

%%metro grid: source | 0,0
%%metro grid: blocker | 1,0
%%metro grid: target | 2,2

graph LR
    subgraph source [Source]
        s1[Input]
        s2[Output]
        s1 -->|a| s2
    end

    subgraph blocker [Blocker]
        b1[Process]
        b2[Output]
        b1 -->|a| b2
    end

    subgraph target [Target]
        %%metro entry: right | a
        t1[Process]
        t2[Output]
        t1 -->|a| t2
    end

    s2 -->|a| t1

CLI command

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

Rendered map

Corridor Narrow Gap Fallback

A left-entry feed crosses two rows past a wider intervening section whose inter-row gap is too narrow for the corridor's clearance band, so it falls back to the around-below loop clear of that section while the adjacent feeder takes the corridor (issue #722).

Mermaid source

%%metro title: Corridor Narrow Gap Fallback
%%metro style: dark
%%metro line: a | A | #e63946
%%metro line: b | B | #0570b0

%%metro grid: source | 2,0
%%metro grid: tall | 2,1
%%metro grid: target | 1,2

graph LR
    subgraph source [Source]
        s1[Input]
        s2[Process]
        s1 -->|a,b| s2
    end

    subgraph tall [Tall Section]
        %%metro entry: left | a
        k1[Step A]
        k2[Step B]
        k3[Step C]
        k4[Step D]
        k1 -->|a| k2
        k2 -->|a| k3
        k3 -->|a| k4
    end

    subgraph target [Target]
        %%metro entry: left | a, b
        t1[Process]
        t2[Output]
        t1 -->|a,b| t2
    end

    s2 -->|b| t1
    s2 -->|a| t1
    k4 -->|a| t1

CLI command

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

Rendered map

Around Section Below

Cross-row route to a LEFT-entry target where the natural inter-row channel would cut through an intervening section's bbox. Exercises `_route_around_section_below` (collector-fan-in geometry).

Mermaid source

%%metro title: Around Section Below
%%metro style: dark
%%metro line: a | A | #e63946
%%metro line: b | B | #0570b0

%%metro grid: source | 2,0
%%metro grid: middle | 1,1
%%metro grid: target | 0,2

graph LR
    subgraph source [Source]
        s1[Input]
        s2[Output]
        s1 -->|a,b| s2
    end

    subgraph middle [Middle Row]
        m1[Process]
        m2[Output]
        m1 -->|a| m2
    end

    subgraph target [Target]
        %%metro entry: left | a, b
        t1[Process]
        t2[Output]
        t1 -->|a,b| t2
    end

    s2 -->|a,b| t1
    s2 -->|a| m1

CLI command

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

Rendered map

Inter Row Wrap Clearance

A right-exit bundle wrapping down to a left-entry in the row below. The horizontal run sits centred in the inter-row gap, clear of both the section above and the next row's header.

Mermaid source

%%metro title: Inter-row wrap clearance
%%metro style: dark
%%metro center_ports: true
%%metro line: l1 | Line 1 | #0570b0
%%metro line: l2 | Line 2 | #d62728
%%metro line: l3 | Line 3 | #756bb1
%%metro grid: top | 0,0
%%metro grid: bottom | 0,1

graph LR
    subgraph top [Top section]
        %%metro exit: right | l1, l2, l3
        a_in[ ]
        a1[Step A1]
        a2[Step A2]
        a3[Step A3]
        a_in -->|l1,l2,l3| a1
        a1 -->|l1,l2,l3| a2
        a2 -->|l1,l2,l3| a3
    end

    subgraph bottom [Bottom section]
        %%metro entry: left | l1, l2, l3
        b_in[ ]
        b1[Step B1]
        b2[Step B2]
        b_in -->|l1,l2,l3| b1
        b1 -->|l1,l2,l3| b2
    end

    a3 -->|l1,l2,l3| b_in

CLI command

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

Rendered map

Inter Row Drop Section Clearance

An inter-row drop threading the gap between two packed sections whose internal sub-gaps are offset by less than the routing clearance. The vertical channel sits centred in the overlap, sharing the unavoidable shortfall evenly instead of skimming one section's edge.

Mermaid source

%%metro title: Inter-row drop channel clearance
%%metro line: l1 | Line 1 | #e6007e
%%metro grid: src | 0,0
%%metro grid: top_a, top_b | 1,0
%%metro grid: bot_c, bot_d | 1,1

graph LR
    subgraph src [Source]
        %%metro exit: right | l1
        s1[Start]
    end
    subgraph top_a [Top A]
        %%metro entry: left | l1
        %%metro exit: right | l1
        a1[Aa]
    end
    subgraph top_b [Top B]
        %%metro entry: left | l1
        b1[Bb]
    end
    subgraph bot_c [Bottom C]
        %%metro entry: left | l1
        c1[Cc]
        c2[Plastid Pi counts]
        c1 -->|l1| c2
    end
    subgraph bot_d [Bottom D]
        %%metro entry: left | l1
        d1[Dd]
    end

    s1 -->|l1| a1
    a1 -->|l1| b1
    a1 -->|l1| d1

CLI command

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

Rendered map

Inter Row Drop Section Clearance Row1

The same offset packed-section squeeze as inter_row_drop_section_clearance, with the wider section in the lower row so the drop would otherwise hug the row-1 section's edge; the channel is centred in the gap instead.

Mermaid source

%%metro title: Inter-row drop channel clearance (row-1 hug)
%%metro line: l1 | Line 1 | #e6007e
%%metro grid: src | 0,0
%%metro grid: top_a, top_b | 1,0
%%metro grid: bot_c, bot_d | 1,1

graph LR
    subgraph src [Source]
        %%metro exit: right | l1
        s1[Start]
    end
    subgraph top_a [Top A]
        %%metro entry: left | l1
        %%metro exit: right | l1
        a1[Aa]
    end
    subgraph bot_c [Bottom C]
        %%metro entry: left | l1
        c1[Cc]
        c2[Plastid Pi counts]
        c1 -->|l1| c2
    end
    subgraph bot_d [Bottom D]
        %%metro entry: left | l1
        d1[Dd]
    end
    subgraph top_b [Top B]
        %%metro entry: left | l1
        b1[Bb]
    end

    s1 -->|l1| a1
    a1 -->|l1| b1
    a1 -->|l1| d1

CLI command

nf-metro render examples/topologies/inter_row_drop_section_clearance_row1.mmd -o inter_row_drop_section_clearance_row1.svg

Rendered map

Cross Col Top Entry

A cross-column feed from a RIGHT-exit producer into a TOP-entry consumer: the entry port is placed on the section boundary rather than floating above the canvas (issue #740).

Mermaid source

%%metro title: Cross-Column Top Entry
%%metro style: dark
%%metro line: l1 | Line 1 | #0570b0

graph LR
    subgraph producer [Producer]
        %%metro exit: right | l1
        p1[Step P1]
        p2[Step P2]
        p1 -->|l1| p2
    end

    subgraph consumer [Consumer]
        %%metro entry: top | l1
        c1[Step C1]
        c2[Step C2]
        c1 -->|l1| c2
    end

    p2 -->|l1| c1

CLI command

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

Rendered map

Lr Top Entry Cross Column

A TB section dropping from its BOTTOM exit into the TOP entry of an LR section whose run sits left of the drop column: the LR run is shifted right under the drop and the section bbox follows it so the trailing station stays contained (issue #1057).

Mermaid source

%%metro title: LR top-entry cross-column drop
%%metro line: a | A | #e63946
%%metro grid: work | 0,0
%%metro grid: out_sec | 0,1
graph LR
    subgraph work [Work]
        %%metro direction: TB
        %%metro exit: bottom | a
        w1[Demux]
        w2[Merge]
        w1 -->|a| w2
    end
    subgraph out_sec [Output]
        %%metro direction: LR
        %%metro entry: top | a
        o1[Publish]
        o2[Notify]
        o1 -->|a| o2
    end
    w2 -->|a| o1

CLI command

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

Rendered map

Lr Top Entry Cross Column Two Line

Two lines dropping together from a TB BOTTOM exit into the TOP entry of an LR section: the in-section line order follows the arrival order so the entry corner nests concentrically and the bundle neither pinches nor crosses through the bend (issue #1061).

Mermaid source

%%metro title: TB perp exit into LR top-entry, two lines
%%metro line: a | A | #e63946
%%metro line: b | B | #0570b0
%%metro grid: work | 0,0
%%metro grid: out_sec | 0,1
graph LR
    subgraph work [Work]
        %%metro direction: TB
        %%metro exit: bottom | a,b
        w1[Demux]
        w2[Merge]
        w1 -->|a,b| w2
    end
    subgraph out_sec [Output]
        %%metro direction: LR
        %%metro entry: top | a,b
        o1[Publish]
        o2[Notify]
        o1 -->|a,b| o2
    end
    w2 -->|a,b| o1

CLI command

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

Rendered map

Right Entry Wrap No Fan

A single line wrapping from an LR exit into a cross-row RL section's RIGHT entry, with no junction siblings (the solo `_route_right_entry_wrap` lead-in).

Mermaid source

%%metro title: Right Entry Wrap No Fan
%%metro style: dark
%%metro line: a | A | #e63946
%%metro grid: source | 0,0
%%metro grid: target | 1,1

graph LR
    subgraph source [Source]
        s1[Start]
        s2[Process]
        s1 -->|a| s2
    end

    subgraph target [Target]
        %%metro direction: RL
        %%metro entry: right | a
        t1[Step One]
        t2[Step Two]
        t1 -->|a| t2
    end

    s2 -->|a| t1

CLI command

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

Rendered map

Left Entry Up Wrap

A two-line bundle wrapping up-and-left from a source below-and-right into a cross-row section's LEFT entry (the `_route_left_entry_wrap` up-riser path); the bundle order is preserved concentrically around the wrap.

Mermaid source

%%metro title: Left-entry up-wrap bundle
%%metro style: dark
%%metro line: w1 | W1 | #e63946
%%metro line: w2 | W2 | #0570b0
%%metro grid: left_tgt | 0,0
%%metro grid: right_src | 1,1
graph LR
    subgraph left_tgt [Left Target]
        %%metro entry: left | w1, w2
        lt1[Collect]
        lt2[Output]
        lt1 -->|w1,w2| lt2
    end
    subgraph right_src [Right Source]
        rs1[Input R]
        rs2[Hub R]
        rs1 -->|w1,w2| rs2
    end
    rs2 -->|w1,w2| lt1

CLI command

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

Rendered map

Around Below Ep Col Gt0

A two-line bundle looping around below the canvas into a non-zero-column LEFT-entry target, past an intervening middle-row section that blocks the direct wrap.

Mermaid source

%%metro title: Around Section Below Ep Col
%%metro style: dark
%%metro line: a | A | #e63946
%%metro line: b | B | #0570b0

%%metro grid: source | 3,0
%%metro grid: middle | 2,1
%%metro grid: target | 1,2

graph LR
    subgraph source [Source]
        s1[Input]
        s2[Output]
        s1 -->|a,b| s2
    end

    subgraph middle [Middle Row]
        m1[Process]
        m2[Output]
        m1 -->|a| m2
    end

    subgraph target [Target]
        %%metro entry: left | a, b
        t1[Process]
        t2[Output]
        t1 -->|a,b| t2
    end

    s2 -->|a,b| t1
    s2 -->|a| m1

CLI command

nf-metro render examples/topologies/around_below_ep_col_gt0.mmd -o around_below_ep_col_gt0.svg

Rendered map

Stacked Left Exit Drop

A LEFT exit feeding a LEFT entry stacked directly below it: the connector leads out into a clean channel left of the column and drops, rather than dropping straight down the shared edge through the source box.

Mermaid source

%%metro title: Stacked Left Exit Drop
%%metro style: dark
%%metro line: a | A | #e63946

%%metro grid: sec1 | 0,0
%%metro grid: sec2 | 0,1

graph LR
    subgraph sec1 [Section 1]
        %%metro direction: RL
        %%metro exit: left | a
        s1[Start]
        s2[Step]
        s1 -->|a| s2
    end

    subgraph sec2 [Section 2]
        %%metro entry: left | a
        t1[Final]
        t2[Done]
        t1 -->|a| t2
    end

    s2 -->|a| t1

CLI command

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

Rendered map

Right Entry From Above

A RIGHT entry whose consumer is the section's flow-start station: the section flows right-to-left so the consumer sits at the entry edge and the feed enters beside it, rather than running across the box to the far station and folding back (#885). Fed from a higher row past the target's right edge, the line drops straight down its outward side to the entry Y rather than looping below the box (#889).

Mermaid source

%%metro title: Right Entry From Above
%%metro style: nfcore
%%metro line: a | A | #e63946
%%metro grid: src | 1,0
%%metro grid: tgt | 0,1

graph LR
    subgraph src [Source]
        s1[Step 1]
        s2[Step 2]
        s1 -->|a| s2
    end

    subgraph tgt [Target]
        %%metro entry: right | a
        t1[Process]
        t2[Output]
        t1 -->|a| t2
    end

    s2 -->|a| t1

CLI command

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

Rendered map

Right Entry From Above Far

A RIGHT entry fed from two rows up, past the target's right edge: the line drops straight down its outward side across the empty intervening row to the entry Y and turns in, rather than diving below the box and climbing back up (#889).

Mermaid source

%%metro title: Right Entry From Above (Far Drop)
%%metro style: nfcore
%%metro line: a | A | #e63946
%%metro grid: src | 1,0
%%metro grid: tgt | 0,2

graph LR
    subgraph src [Source]
        s1[Step 1]
        s2[Step 2]
        s1 -->|a| s2
    end

    subgraph tgt [Target]
        %%metro entry: right | a
        t1[Process]
        t2[Output]
        t1 -->|a| t2
    end

    s2 -->|a| t1

CLI command

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

Rendered map

Route Around Intervening

A line skips a middle section: it routes around the intervening section's bbox rather than slicing through it.

Mermaid source

%%metro title: Route Around Intervening
%%metro style: dark
%%metro line: trunk | Trunk | #0570b0
%%metro line: skip | Skip | #e63946

%%metro grid: source | 0,0
%%metro grid: middle | 1,0
%%metro grid: target | 2,0

graph LR
    subgraph source [Source]
        s1[Input]
        s2[Output]
        s1 -->|trunk,skip| s2
    end

    subgraph middle [Middle]
        m1[Process]
        m2[Output]
        m1 -->|trunk| m2
    end

    subgraph target [Target]
        t1[Collect]
        t2[Report]
        t1 -->|trunk,skip| t2
    end

    s2 -->|trunk| m1
    m2 -->|trunk| t1
    s2 -->|skip| t1

CLI command

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

Rendered map

Cross Row Gap Wrap

A cross-row feed runs its horizontal in the inter-row gap and drops straight in, rather than diving under the return row counter to its flow.

Mermaid source

%%metro title: Cross-Row Gap Wrap
%%metro style: dark
%%metro line: main | Main | #0570b0
%%metro line: feed | Feed | #e63946
%%metro fold_threshold: 8

graph LR
    subgraph ingest [Ingest]
        i1[Read]
        i2[QC]
        i1 -->|main,feed| i2
    end

    subgraph align [Align]
        a1[Map]
        a2[Sort]
        a1 -->|main| a2
    end

    subgraph dedup [Dedup]
        d1[Mark]
        d2[Recal]
        d1 -->|main| d2
    end

    subgraph merge_pt [Merge]
        g1[Combine]
        g2[Refine]
        g1 -->|main,feed| g2
    end

    subgraph report [Report]
        rp1[Summarise]
        rp2[Publish]
        rp1 -->|main| rp2
    end

    i2 -->|main| a1
    a2 -->|main| d1
    d2 -->|main| g1
    i2 -->|main| g1
    g2 -->|main| rp1
    i2 -->|feed| g1

CLI command

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

Rendered map

Rl Entry Runway

A source section feeding a left-hand target via `%%metro exit: left`: it flows right-to-left so its producers sit at the left exit edge and the runway leaves beside them, rather than the producers exiting left back through the start station (#885).

Mermaid source

%%metro title: RL Entry Runway
%%metro style: dark
%%metro line: l1 | L1 | #2db572
%%metro line: l2 | L2 | #e63946
%%metro grid: rl_sec | 0,0
%%metro grid: src_sec | 1,0

graph LR
    subgraph src_sec [Source]
        %%metro exit: left | l1,l2
        s1[Start]
        s2[Prep A]
        s3[Prep B]
        s1 -->|l1| s2
        s1 -->|l2| s3
    end

    subgraph rl_sec [RL Section]
        %%metro direction: RL
        %%metro entry: right | l1,l2
        r1[Stage One]
        r2[Stage Two]
        r3[Stage Three]
        r4[Deep Target]
        r1 -->|l1| r2
        r2 -->|l1| r3
        r3 -->|l1| r4
        r1 -->|l2| r2
    end

    s2 -->|l1| r4
    s3 -->|l2| r1

CLI command

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

Rendered map

Lr Perp Top Exit Side Entry

Two co-travelling lines leave an LR section through an explicit TOP exit and feed the LEFT entry of a same-row neighbour. The exit port sits past the last station, and the bundle rises into the header band, runs across, and descends to the consumer's row to enter straight, staying parallel through every concentric corner.

Mermaid source

%%metro title: LR Perp Top Exit into Side Entry
%%metro style: dark
%%metro line: a | Line A | #e63946
%%metro line: b | Line B | #0570b0

graph LR
    subgraph src [Source]
        s1[Start]
    end

    subgraph mid [Middle]
        %%metro exit: top | a, b
        m1[Step 1]
        m2[Step 2]
        m1 -->|a,b| m2
    end

    subgraph dst [Destination]
        d1[Finish]
    end

    s1 -->|a,b| m1
    m2 -->|a,b| d1

CLI command

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

Rendered map

Lr Perp Bottom Exit Side Entry

The BOTTOM-exit mirror of lr_perp_top_exit_side_entry: the bundle drops below the source section, runs across the under-row band, and rises back to the consumer's row to enter straight.

Mermaid source

%%metro title: LR Perp Bottom Exit into Side Entry
%%metro style: dark
%%metro line: a | Line A | #e63946
%%metro line: b | Line B | #0570b0

graph LR
    subgraph src [Source]
        s1[Start]
    end

    subgraph mid [Middle]
        %%metro exit: bottom | a, b
        m1[Step 1]
        m2[Step 2]
        m1 -->|a,b| m2
    end

    subgraph dst [Destination]
        d1[Finish]
    end

    s1 -->|a,b| m1
    m2 -->|a,b| d1

CLI command

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

Rendered map

Lr Perp Top Exit Perp Entry

Two co-travelling lines leave an LR section through a TOP exit and feed the TOP entry of a same-row neighbour in another column. The bundle rises over the header band and drops into the consumer trunk, keeping a single left/right order across the shared entry port so it stays parallel without crossing at the drop.

Mermaid source

%%metro title: Cross-Column Perp Entry
%%metro style: dark
%%metro line: main | Main | #e63946
%%metro line: branch | Branch | #2db572

graph LR
    subgraph src [Source]
        %%metro exit: right | main,branch
        s1[Start]
    end
    subgraph sec1 [Section One]
        %%metro entry: left | main,branch
        %%metro exit: top | main,branch
        a[Input]
        b[Output]
        a -->|main,branch| b
    end
    subgraph sec2 [Section Two]
        %%metro entry: top | main,branch
        d[Step D]
        e[Step E]
        d -->|main,branch| e
    end
    s1 -->|main,branch| a
    b -->|main,branch| d

CLI command

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

Rendered map

Lr Perp Bottom Exit Perp Entry

The BOTTOM-exit mirror of lr_perp_top_exit_perp_entry: the bundle drops under the row, runs across, and rises into the consumer's BOTTOM entry, staying parallel through the corridor.

Mermaid source

%%metro title: Cross-Column Perp Bottom Entry
%%metro style: dark
%%metro line: main | Main | #e63946
%%metro line: branch | Branch | #2db572

graph LR
    subgraph src [Source]
        %%metro exit: right | main,branch
        s1[Start]
    end
    subgraph sec1 [Section One]
        %%metro entry: left | main,branch
        %%metro exit: bottom | main,branch
        a[Input]
        b[Output]
        a -->|main,branch| b
    end
    subgraph sec2 [Section Two]
        %%metro entry: bottom | main,branch
        d[Step D]
        e[Step E]
        d -->|main,branch| e
    end
    s1 -->|main,branch| a
    b -->|main,branch| d

CLI command

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

Rendered map

Lr Perp Top Exit Perp Entry Diverging

A TOP-exit bundle taken over the corridor into a TOP entry where the two lines split to different downstream stations. Consistent corridor ordering routes each line to its target without a convergence jog at the entry.

Mermaid source

%%metro title: Cross-Column Perp Entry Diverging
%%metro style: dark
%%metro line: main | Main | #e63946
%%metro line: branch | Branch | #2db572

graph LR
    subgraph src [Source]
        %%metro exit: right | main,branch
        s1[Start]
    end
    subgraph sec1 [Section One]
        %%metro entry: left | main,branch
        %%metro exit: top | main,branch
        a[Input]
        b[Output]
        a -->|main,branch| b
    end
    subgraph sec2 [Section Two]
        %%metro entry: top | main,branch
        d[Step D]
        e[Step E]
        d -->|main| e
    end
    s1 -->|main,branch| a
    b -->|main| d
    b -->|branch| e

CLI command

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

Rendered map

Cross Column Perp Drop

A `%%metro direction: TB` section fed by a perpendicular drop from a section in a different grid column. The vertical trunk stays on the QC section's own column and the cross-column feed comes over the top and drops into the trunk head, rather than the trunk being dragged out toward the off-column source.

Mermaid source

%%metro title: Cross-column perpendicular drop
%%metro line: reads | Reads | #1f77b4

graph LR
    subgraph align [Alignment]
        %%metro exit: top | reads
        load[Load]
        trim[Trim]
        bwa[BWA-MEM]
        load -->|reads| trim
        trim -->|reads| bwa
    end
    subgraph qc [QC report]
        %%metro direction: TB
        %%metro entry: top | reads
        collect[Collect]
        multiqc[MultiQC]
        collect -->|reads| multiqc
    end
    bwa -->|reads| collect

CLI command

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

Rendered map

Cross Column Perp Drop Far Exit

The cross-column perpendicular drop where the source's exit side faces away from the target's entry side (a BOTTOM exit feeding a TOP entry). The lead-in crosses to the inter-column gap and reaches the TOP entry from above the box, rather than rising up the trunk through the section's stations.

Mermaid source

%%metro title: Cross-column perpendicular drop (far-side exit)
%%metro line: reads | Reads | #1f77b4

graph LR
    subgraph align [Alignment]
        %%metro exit: bottom | reads
        load[Load]
        trim[Trim]
        bwa[BWA-MEM]
        load -->|reads| trim
        trim -->|reads| bwa
    end
    subgraph qc [QC report]
        %%metro direction: TB
        %%metro entry: top | reads
        collect[Collect]
        multiqc[MultiQC]
        collect -->|reads| multiqc
    end
    bwa -->|reads| collect

CLI command

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

Rendered map

Bottom Row Climb Clear Corridor

A section in the bottommost grid row sends a line up and across to a higher-row target several columns away. The columns it spans hold no same-row section, so the line runs along its own row level and climbs at the end rather than diving below the source row to the canvas floor and looping back up.

Mermaid source

%%metro title: Bottom-row climb over a clear corridor
%%metro style: dark
%%metro line: main | Main | #2db572
%%metro line: side | Side | #ff8c00
%%metro grid: feed | 0,0
%%metro grid: mid_a | 2,0
%%metro grid: mid_b | 3,0
%%metro grid: dest | 4,0
%%metro grid: low | 1,1

graph LR
    subgraph feed [Feed]
        a[A]
    end

    subgraph low [Low]
        x[X]
    end

    subgraph mid_a [Mid A]
        m[M]
    end

    subgraph mid_b [Mid B]
        n[N]
    end

    subgraph dest [Dest]
        z[Z]
    end

    a -->|main| m
    m -->|main| n
    n -->|main| z

    a -->|side| x
    x -->|side| z

CLI command

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

Rendered map

Multicarrier Offrow Exit Climb

A section's exit port carries two lines from two stations that share a trunk row off the port row, then fans out through a junction to several rows. The parallel bundle anchors on the shared carrier row so it runs flat inside the section and the fan-out risers fall in the inter-section gap, rather than both lines climbing a diagonal up to the port inside the section.

Mermaid source

%%metro title: Multi-carrier off-row exit climb
%%metro style: dark
%%metro line: ubam | uBAM | #0570b0
%%metro line: fastq | FASTQ | #2db572
%%metro line: bam | BAM | #f5c542
%%metro line: other | Other | #ff8c00
%%metro files: fastq_in | FASTQ
%%metro files: bam_in | BAM
%%metro files: ubam_in | uBAM
%%metro grid: prep | 0,0
%%metro grid: variants | 1,0
%%metro grid: depth | 1,1

graph LR
    subgraph prep [Pre-processing]
        fastq_in[ ]
        bam_in[ ]
        ubam_in[ ]
        cat_fastq[cat FASTQ]
        samtools_merge[samtools\nmerge]
        minimap2_align[minimap2]
        samtools_sort_index[samtools\nsort/index]
        mosdepth[mosdepth]

        fastq_in -->|fastq| cat_fastq
        ubam_in -->|ubam| samtools_merge
        bam_in -->|bam| samtools_merge
        cat_fastq -->|fastq| minimap2_align
        samtools_merge -->|ubam| minimap2_align
        minimap2_align -->|bam| samtools_sort_index
        samtools_merge -->|bam| samtools_sort_index
        samtools_sort_index -->|bam| mosdepth
    end
    subgraph variants [Small variant calling]
        clair3[Clair3]
        deepvariant[Deepvariant]
    end
    subgraph depth [Depth & repeats]
        longtr[LongTR]
        ontspectre[ont-spectre]
    end
    samtools_sort_index -->|bam| clair3
    samtools_sort_index -->|bam| deepvariant
    samtools_sort_index -->|bam| longtr
    mosdepth -->|other| ontspectre

CLI command

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

Rendered map

Clear Channel Target Aware Push

A hub fans one line down into a wide section stacked directly below and another down-and-right to a target. The fan descent for the rightward line grazes the wide block, so the graze correction pushes it toward the target's side of the block rather than the nearer edge, keeping the line heading to its target instead of detouring across the canvas.

Mermaid source

%%metro title: Fan descent target-aware push
%%metro line: dna | DNA | #2db572
%%metro line: rna | RNA | #e63946

%%metro grid: src | 0,0
%%metro grid: block | 0,1
%%metro grid: target | 1,2

graph LR
    subgraph src [Src]
        s_in[I]
        s_hub[H]
        s_in -->|dna,rna| s_hub
    end
    subgraph block [Block]
        b_a[A]
        b_b[B]
        b_c[C]
        b_d[D]
        b_e[E]
        b_f[F]
        b_a -->|dna| b_b
        b_b -->|dna| b_c
        b_c -->|dna| b_d
        b_d -->|dna| b_e
        b_e -->|dna| b_f
    end
    subgraph target [Target]
        %%metro entry: left | rna
        t_a[T1]
        t_b[T2]
        t_a -->|rna| t_b
    end
    s_hub -->|rna| t_a
    s_hub -->|dna| b_a

CLI command

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

Rendered map

Near Vertical Junction Hook

A fan-out junction overhanging a same-column RIGHT entry one row below. The two-line bundle drops straight down the junction's own column and turns once into the port, rather than leading out to a centred gap channel and hooking back: a hook's opposite-handed corners cannot nest a multi-line bundle. The destination section carries the matching line order so the bundle arrives in the order the section lays it out (#1018).

Mermaid source

%%metro title: Near-Vertical Junction Hook
%%metro style: nfcore
%%metro line: main | Main | #2db572
%%metro line: a | A | #e63946
%%metro line: b | B | #7b2d3b
%%metro grid: src | 0,0
%%metro grid: gen | 1,0
%%metro grid: pseudo | 0,1

graph LR
    subgraph src [Source]
        s1[Step 1]
        s2[Step 2]
        s3[Step 3]
        s1 -->|main,a,b| s2
        s2 -->|main,a,b| s3
    end

    subgraph gen [Genome]
        g1[Genome]
    end

    subgraph pseudo [Pseudo]
        %%metro entry: right | a, b
        p1[Pseudo 1]
        p2[Pseudo 2]
        p3[Pseudo 3]
        p1 -->|a,b| p2
        p2 -->|a,b| p3
    end

    s3 -->|main| g1
    s3 -->|a,b| p1

CLI command

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

Rendered map

Near Edge Exit Corner

A station one column short of its section's right edge whose exit port sits on that edge, one lane below it. Equalising the station's flat runs must not push the exit's approach corner past the port: the corner stays inside the box so the line turns down through the port cleanly rather than bulging outside the section and doubling back (issue #1314).

Mermaid source

%%metro title: Near-edge exit corner
%%metro line: riboseq | Ribo-seq | #e6007e
%%metro line: rnaseq | RNA-seq | #2db572

graph LR
    subgraph psite_id [P-site identification]
        ribowaltz[riboWaltz]
        plastid_wiggle[plastid Wiggle]
        psite_counts[Plastid P-site counts]
        quantify_orf_psite[Quantify ORF P-sites]

        ribowaltz -->|riboseq| report_ribowaltz[riboWaltz report]
        plastid_psite[plastid P-site] -->|riboseq| plastid_wiggle
        plastid_wiggle -->|riboseq| psite_counts
        orf_catalogue[ORF catalogue] -->|riboseq| quantify_orf_psite
        plastid_wiggle -->|riboseq| quantify_orf_psite
    end
    subgraph te [Translational efficiency]
        dte_counts_prep[Prep ORF TE counts] -->|riboseq,rnaseq| deltate_orf[DESeq2 deltaTE]
        dte_counts_prep -->|riboseq,rnaseq| dotseq_orf[DOTSeq]
    end
    psite_counts -->|riboseq| te_counts_prep[Prep TE counts]
    quantify_orf_psite -->|riboseq| dte_counts_prep

CLI command

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

Rendered map

Bypass Routing

Inrow Skip Breeze

An express line skips a station three collinear stations share; the geometric bypass pass bows it around the skipped marker (#990).

Mermaid source

%%metro title: In-row express skip
%%metro style: dark
%%metro line: a | Local | #2db572
%%metro line: b | Express | #e63946
graph LR
    subgraph s [Section]
        s1[S1]
        s2[S2]
        s3[S3]
        s1 -->|a| s2
        s2 -->|a| s3
        s1 -->|b| s3
    end

CLI command

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

Rendered map

Sectionless Skip Breeze

A skip-line jumps between two stops on a graph with no declared section, skipping the stops between them. Interchange inference detects the parallel-lane hub and the detour routes around the skipped markers instead of through them (#1229).

Mermaid source

%%metro title: Sectionless express skip
%%metro style: dark
%%metro line: main | Main | #e63946
%%metro line: alt | Alt | #1d4e89
graph LR
    a[A]
    b[B]
    c[C]
    d[D]
    e[E]
    a -->|main| b
    b -->|main| c
    c -->|main| d
    d -->|main| e
    a -->|alt| c
    c -->|alt| e

CLI command

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

Rendered map

Interchange Label Clears Bridge

An in-section skip infers a two-member interchange at C, drawn with a vertical connector bridge between its rails. C's label clears the whole bridge (below the far track) instead of landing on it, where plain layer alternation would drop it (#1239).

Mermaid source

%%metro title: In-section express skip
%%metro style: dark
%%metro line: main | Main | #e63946
%%metro line: alt | Alt | #1d4e89
graph LR
    subgraph sec [Section]
        a[A]
        b[B]
        c[C]
        d[D]
        e[E]
        a -->|main| b
        b -->|main| c
        c -->|main| d
        d -->|main| e
        a -->|alt| c
        c -->|alt| e
    end

CLI command

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

Rendered map

Bypass Fan In Outer Slot

A bypass line (QC) skips hub and alignment to reach a deeper station (MultiQC Report) in the Integration section, while dna/meth/rna/atac converge at a fan-in entry port. The bypass line claims the outer slot so no empty interior gaps appear (issue #655).

Mermaid source

%%metro title: Bypass Fan-in Outer Slot
%%metro style: dark
%%metro line: dna | DNA | #e63946
%%metro line: meth | Methylation | #0570b0
%%metro line: rna | RNA | #2db572
%%metro line: atac | ATAC | #f5c542
%%metro line: qc | QC | #ff8c00

graph LR
    subgraph ingest [Ingest]
        samplesheet[Samplesheet]
        demux[Demultiplex]
        samplesheet -->|dna,meth,rna,atac,qc| demux
    end

    subgraph trim [Trim & QC]
        fastp[Fastp]
        screen[Contam Screen]
        fastp -->|dna,meth,rna,atac,qc| screen
    end

    subgraph hub [Branch Hub]
        dispatch[Dispatch]
    end

    subgraph align_right [Alignment]
        bwa[BWA-MEM]
        markdup[MarkDup]
        bwa -->|dna,meth| markdup
    end

    subgraph quant_bottom [Quantification]
        salmon[Salmon]
        tximport[Tximport]
        salmon -->|rna| tximport
    end

    subgraph peaks_bottom [Peak Calling]
        macs[MACS2]
        macs -->|atac| macs2anno[Annotate Peaks]
    end

    subgraph integrate [Integration]
        mofa[MOFA Factor Model]
        report[MultiQC Report]
        mofa -->|dna,meth,rna,atac| report
    end

    demux -->|dna,meth,rna,atac,qc| fastp
    screen -->|dna,meth,rna,atac,qc| dispatch

    dispatch -->|dna,meth| bwa
    dispatch -->|rna| salmon
    dispatch -->|atac| macs

    markdup -->|dna,meth| mofa
    tximport -->|rna| mofa
    macs2anno -->|atac| mofa

    screen -->|qc| report

CLI command

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

Rendered map

Upward Bypass

Tall section bypass where the trunk is above the source (upward gap1).

Mermaid source

%%metro title: Upward Bypass Test
%%metro style: dark
%%metro line: a | Line A | #FF9800
%%metro line: b | Line B | #4CAF50
%%metro line: c | Line C | #2196F3
%%metro line: d | Line D | #E91E63
%%metro line: e | Line E | #9C27B0
%%metro line: f | Line F | #00BCD4
%%metro line: g | Line G | #CDDC39

graph LR
    subgraph input [Input]
        hub[Hub]
    end

    subgraph wide [Wide Fan-out]
        w1[Tool 1]
        w2[Tool 2]
        w3[Tool 3]
        w4[Tool 4]
        w5[Tool 5]
        w6[Tool 6]
        w7[Tool 7]
    end

    subgraph adjacent [Adjacent]
        adj[Collect]
    end

    subgraph far [Far Target]
        out[Output]
    end

    hub -->|a| w1
    hub -->|b| w2
    hub -->|c| w3
    hub -->|d| w4
    hub -->|e| w5
    hub -->|f| w6
    hub -->|g| w7

    %% Adjacent (L-shape)
    w1 -->|a| adj

    %% Bypass: bottom of wide -> far (skipping adjacent)
    w1 -->|a| out
    w2 -->|b| out
    w3 -->|c| out
    w4 -->|d| out
    w5 -->|e| out
    w6 -->|f| out
    w7 -->|g| out

    adj -->|a| out

CLI command

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

Rendered map

Bypass Label Rake

A foreign line dips below a station to bypass its marker, then climbs back to the trunk past the wide 'Quantification' label. The router lengthens the dip's flat run so the climb seats clear of the glyphs (`_clear_bypass_v_label_strikes`).

Mermaid source

%%metro title: Bypass V Past A Wide Label
%%metro style: dark
%%metro line: dna | DNA | #e63946
%%metro line: rna | RNA | #0570b0
%%metro line: prot | Protein | #2db572

graph LR
    subgraph input [Input]
        fetch[Fetch Data]
        validate[Validate]
        fetch -->|dna,rna,prot| validate
    end

    subgraph processing [Processing]
        branch[Branch]
        align[Alignment]
        quant[Quantification]
        search[Database Search]
        branch -->|dna,rna| align
        branch -->|prot| search
        align -->|rna| quant
    end

    subgraph reporting [Reporting]
        multiqc[MultiQC]
    end

    validate -->|dna,rna,prot| branch
    align -->|dna| multiqc
    quant -->|rna| multiqc
    search -->|prot| multiqc

CLI command

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

Rendered map

Bypass Label Rake Left

Mirror of the bypass-label rake: the dip's descending leg, not its climb, crosses the wide 'Quantification Step' label, so its V corner lands in the label's left half and the router seats it clear of the left edge (`_clear_bypass_v_label_strikes`).

Mermaid source

%%metro title: Bypass V Past A Wide Label (Left Overrun)
%%metro style: dark
%%metro line: dna | DNA | #e63946
%%metro line: rna | RNA | #0570b0
%%metro line: prot | Protein | #2db572

graph LR
    subgraph input [Input]
        fetch[Fetch Data]
        validate[Validate]
        fetch -->|dna,rna,prot| validate
    end

    subgraph processing [Processing]
        branch[Branch]
        align[Alignment]
        quant[Quantification Step]
        search[Hits]
        branch -->|dna,rna| align
        branch -->|prot| search
        align -->|rna| quant
    end

    subgraph reporting [Reporting]
        multiqc[MultiQC]
    end

    validate -->|dna,rna,prot| branch
    align -->|dna| multiqc
    quant -->|rna| multiqc
    search -->|prot| multiqc

CLI command

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

Rendered map

Bypass Label Rake Wide

An extra-wide bypassed-station label the router cannot seat the V's flat-run corner clear of: the strike-clearance loop pushes the bypassed node out by whole grid columns until the dip clears the glyphs, widening rather than relying on the router's partial corner-seating (issue #700).

Mermaid source

%%metro title: Bypass V Past An Extra-Wide Label
%%metro style: dark
%%metro line: dna | DNA | #e63946
%%metro line: rna | RNA | #0570b0
%%metro line: prot | Protein | #2db572

graph LR
    subgraph input [Input]
        fetch[Fetch Data]
        validate[Validate]
        fetch -->|dna,rna,prot| validate
    end

    subgraph processing [Processing]
        branch[Branch]
        align[Alignment]
        quant[Quantification And Expression Estimation Module]
        search[Database Search]
        branch -->|dna,rna| align
        branch -->|prot| search
        align -->|rna| quant
    end

    subgraph reporting [Reporting]
        multiqc[MultiQC]
    end

    validate -->|dna,rna,prot| branch
    align -->|dna| multiqc
    quant -->|rna| multiqc
    search -->|prot| multiqc

CLI command

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

Rendered map

Bypass V Tight

An intra-section bypass V at a tight column pitch: without room for a lead-in the descent would diverge on the 'Process A' marker and rake its label. The engine pushes the bypassed node to a further grid column so the V diverges past the label and keeps a visible flat run through its X (issue #688).

Mermaid source

%%metro title: Bypass V Tight
%%metro style: dark
%%metro x_spacing: 50
%%metro line: a | Line A | #FF9800
%%metro line: b | Line B | #4CAF50

graph LR
    subgraph src [Source]
        s1[Start]
    end
    subgraph mid [Mid]
        %%metro exit: right | a,b
        m1[Process A]
        m2[Transform]
        m1 -->|a| m2
    end
    subgraph dest [Dest]
        d1[End]
    end

    s1 -->|a,b| m1
    m2 -->|a| d1
    m1 -->|b| d1

CLI command

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

Rendered map

Fan Bypass Nesting

A junction fans to a straight continuation, three down-turns into stacked rows, and one far-column bypass. The bypass joins the same concentric corner as the down-turns and descends in the shared channel, peeling into its lane at the inter-row gap rather than grazing the down-turn corners near the junction (issue #652).

Mermaid source

%%metro title: Fan-out + bypass nesting
%%metro line: dna | DNA | #2db572
%%metro line: rna | RNA | #e63946
%%metro line: qc | QC | #f4a261

graph LR
    subgraph src [Source]
        s_in[In]
        s_hub[Hub]
        s_in -->|dna,rna,qc| s_hub
    end

    subgraph straight [Straight]
        st_a[A]
        st_b[B]
        st_a -->|dna| st_b
    end

    subgraph down1 [Down 1]
        d1_a[C1]
        d1_b[C2]
        d1_a -->|dna| d1_b
    end

    subgraph down2 [Down 2]
        d2_a[E1]
        d2_b[E2]
        d2_a -->|rna| d2_b
    end

    subgraph down3 [Down 3]
        d3_a[F1]
        d3_b[F2]
        d3_a -->|rna| d3_b
    end

    subgraph mid [Mid]
        m_a[M1]
        m_b[M2]
        m_a -->|dna,rna| m_b
    end

    subgraph sink [Report]
        rp_a[R1]
        rp_b[R2]
        rp_a -->|dna,rna,qc| rp_b
    end

    s_hub -->|dna| st_a
    s_hub -->|dna| d1_a
    s_hub -->|rna| d2_a
    s_hub -->|rna| d3_a
    s_hub -->|qc| rp_a
    d1_b -->|dna| m_a
    d2_b -->|rna| m_a
    d3_b -->|rna| m_a
    m_b -->|dna,rna| rp_a

CLI command

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

Rendered map

Divergent Fanout Split

One line fans out from a single source to a near and a far target in the row below. The two descents stay fused as one trunk until the near branch turns off, so the farther branch never peels onto the inside of the nearer one and crosses it (issue #702).

Mermaid source

%%metro title: Divergent Fanout Split
%%metro style: dark
%%metro line: main | Main | #0570b0
%%metro grid: src | 0,0
%%metro grid: nearrow | 1,1
%%metro grid: farrow | 2,1

graph LR
    subgraph src [Source]
        %%metro exit: right | main
        s1[Input]
        s2[Process]
        s1 -->|main| s2
    end
    subgraph nearrow [Near Target]
        %%metro entry: left | main
        n1[NearStep]
    end
    subgraph farrow [Far Target]
        %%metro entry: left | main
        f1[Collect]
        f2[Report]
        f1 -->|main| f2
    end
    s2 -->|main| n1
    s2 -->|main| f1

CLI command

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

Rendered map

Disjoint Sameline Trunks

Two lines diving into one below-row channel to bypass a section ride a tight concentric bundle until a member peels up at its turn column, rather than being split apart by a track reserved for a trunk that only appears further along the channel (issue #702).

Mermaid source

%%metro title: Disjoint Same-Line Bypass Trunks
%%metro style: dark
%%metro line: a | Line A | #e63946
%%metro line: b | Line B | #2db572
%%metro line: c | Line C | #0570b0
%%metro grid: secA | 0,0
%%metro grid: secB | 1,0
%%metro grid: secC | 2,0
%%metro grid: secD | 3,0
%%metro grid: secE | 4,0

graph LR
    subgraph secA [Ingest]
        %%metro exit: right | a, b, c
        a_node[Input]
    end

    subgraph secB [QC]
        %%metro entry: left | b
        %%metro exit: right | b
        b_node[QC Step]
    end

    subgraph secC [Align]
        %%metro entry: left | a, b
        %%metro exit: right | a, b
        c_node[Align]
    end

    subgraph secD [Call]
        %%metro entry: left | c
        %%metro exit: right | c
        d_node[Call]
    end

    subgraph secE [Report]
        %%metro entry: left | a, b, c
        e_node[Report]
    end

    a_node -->|b| b_node
    a_node -->|a| c_node
    a_node -->|c| d_node
    b_node -->|b| c_node
    c_node -->|a,b| e_node
    d_node -->|c| e_node

CLI command

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

Rendered map

Dogleg Exempt Distinct

A bypass line cleared off a different line's exempt wrap trunk in the inter-row gap runs parallel above it as a tight bundle, rather than doglegging onto the crossing side where its riser would pierce the wrap run twice (issue #702).

Mermaid source

%%metro title: Dogleg Off Exempt Trunks - Distinct Line Regime
%%metro style: dark
%%metro line: wrap | Wrap | #0570b0
%%metro line: byp | Bypass | #e63946
%%metro line: skip | Skip | #2ca02c

%%metro grid: left_tgt | 0,0
%%metro grid: right_src | 1,1
%%metro grid: bot_sink | 2,1
%%metro grid: skip_src | 0,1

graph LR
    subgraph left_tgt [Left Target]
        %%metro entry: left | wrap
        lt1[Collect]
        lt2[Output]
        lt1 -->|wrap| lt2
    end

    subgraph right_src [Right Source]
        rs1[Input R]
        rs2[Hub R]
        rs1 -->|wrap| rs2
    end

    subgraph bot_sink [Bottom Sink]
        bs1[Collect B]
        bs2[Output B]
        bs1 -->|byp| bs2
    end

    subgraph skip_src [Skip Source]
        ss1[Step S]
        ss2[Out S]
        ss1 -->|skip| ss2
    end

    rs2 -->|wrap| lt1
    lt2 -->|byp| bs1
    ss2 -->|skip| bs1

CLI command

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

Rendered map

Dogleg Exempt Sameline

Two opposing flows of one line fused in the inter-row gap are pulled apart into a dogleg; the down-moved trunk stops short of the next row's section header badge, keeping the required clearance rather than crowding it (issue #698).

Mermaid source

%%metro title: Dogleg Off Exempt Trunks - Same Line Regime
%%metro style: dark
%%metro line: wrap | Wrap | #0570b0

%%metro grid: left_tgt | 0,0
%%metro grid: right_src | 1,1
%%metro grid: new_tgt | 2,1

graph LR
    subgraph left_tgt [Left Target]
        %%metro entry: left | wrap
        lt1[Collect]
        lt2[Output]
        lt1 -->|wrap| lt2
    end

    subgraph right_src [Right Source]
        rs1[Input R]
        rs2[Hub R]
        rs1 -->|wrap| rs2
    end

    subgraph new_tgt [New Target]
        nt1[Hub N]
        nt2[Out N]
        nt1 -->|wrap| nt2
    end

    rs2 -->|wrap| lt1
    lt2 -->|wrap| nt1

CLI command

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

Rendered map

Dogleg Twoline Fanout

Two distinct lines leave one section through a shared exit junction to different sections in the row below. They descend as one concentric bundle and split only where the near line peels into its target while the far line continues over it, rather than diverging at the junction and crossing (issue #719).

Mermaid source

%%metro title: Two flows leaving one section
%%metro style: dark
%%metro line: to_src | To Source | #e7298a
%%metro line: to_new | To New | #0570b0

%%metro grid: left_tgt | 0,0
%%metro grid: right_src | 1,1
%%metro grid: new_tgt | 2,1

graph LR
    subgraph left_tgt [Left Target]
        lt1[Collect]
        lt2[Output]
        lt1 -->|to_src,to_new| lt2
    end

    subgraph right_src [Right Source]
        rs1[Input R]
        rs2[Hub R]
        rs1 -->|to_src| rs2
    end

    subgraph new_tgt [New Target]
        nt1[Hub N]
        nt2[Out N]
        nt1 -->|to_new| nt2
    end

    lt2 -->|to_src| rs1
    lt2 -->|to_new| nt1

CLI command

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

Rendered map

Bypass Gap2 Rightward Overflow

A seven-line rightward bypass whose gap-2 bundle right edge overflows the inter-column gap limit and is clamped, keeping the bundle inside the gap.

Mermaid source

%%metro title: Seven-line rightward bypass gap2 overflow clamp
%%metro style: dark
%%metro line: l1 | L1 | #e63946
%%metro line: l2 | L2 | #0570b0
%%metro line: l3 | L3 | #2db572
%%metro line: l4 | L4 | #f4a261
%%metro line: l5 | L5 | #9467bd
%%metro line: l6 | L6 | #8c564b
%%metro line: l7 | L7 | #17becf

%%metro grid: src_sec | 0,0
%%metro grid: mid_sec | 1,0
%%metro grid: tgt_sec | 2,0

graph LR
    subgraph src_sec [Source]
        %%metro exit: right | l1, l2, l3, l4, l5, l6, l7
        s1[Start]
        s2[Out]
        s1 -->|l1,l2,l3,l4,l5,l6,l7| s2
    end

    subgraph mid_sec [Middle]
        m1[Mid]
        m2[MidOut]
        m1 -->|l1| m2
    end

    subgraph tgt_sec [Target]
        %%metro entry: left | l1, l2, l3, l4, l5, l6, l7
        t1[Process]
        t2[End]
        t1 -->|l1,l2,l3,l4,l5,l6,l7| t2
    end

    s2 -->|l1| m1
    s2 -->|l1,l2,l3,l4,l5,l6,l7| t1

CLI command

nf-metro render examples/topologies/bypass_gap2_rightward_overflow.mmd -o bypass_gap2_rightward_overflow.svg

Rendered map

Bypass Leftward Overflow

A seven-line reverse-flow (right-to-left) bypass: the trunk leads out leftward, the mirror of every other bypass. The concentric order and corner radii follow the trunk's travel direction so the bundle fans cleanly instead of twisting at the descent corner (issue #723).

Mermaid source

%%metro title: Seven-line reverse-flow bypass overflow
%%metro style: dark
%%metro line: l1 | L1 | #e63946
%%metro line: l2 | L2 | #0570b0
%%metro line: l3 | L3 | #2db572
%%metro line: l4 | L4 | #f4a261
%%metro line: l5 | L5 | #9467bd
%%metro line: l6 | L6 | #8c564b
%%metro line: l7 | L7 | #17becf

%%metro grid: tgt_sec | 0,0
%%metro grid: mid_sec | 1,0
%%metro grid: src_sec | 2,0

graph LR
    subgraph src_sec [Source]
        %%metro exit: left | l1, l2, l3, l4, l5, l6, l7
        s1[Start]
        s2[Out]
        s1 -->|l1,l2,l3,l4,l5,l6,l7| s2
    end

    subgraph mid_sec [Middle]
        m1[Mid]
        m2[MidOut]
        m1 -->|l1| m2
    end

    subgraph tgt_sec [Target]
        %%metro entry: right | l1, l2, l3, l4, l5, l6, l7
        t1[Process]
        t2[End]
        t1 -->|l1,l2,l3,l4,l5,l6,l7| t2
    end

    s2 -->|l1,l2,l3,l4,l5,l6,l7| t1

CLI command

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

Rendered map

Bypass Leftward Far Side Entry

A seven-line reverse-flow bypass into a far-side LEFT entry: the source exits its left edge and the target's entry port is on its own far (left) edge, so the bundle wraps around below into the port from its outward side. The half-turn transposes the bundle, so the target section's line order is reversed to match and no line crosses a mate (issue #974).

Mermaid source

%%metro title: Seven-line leftward bypass far-side entry
%%metro style: dark
%%metro line: l1 | L1 | #e63946
%%metro line: l2 | L2 | #0570b0
%%metro line: l3 | L3 | #2db572
%%metro line: l4 | L4 | #f4a261
%%metro line: l5 | L5 | #9467bd
%%metro line: l6 | L6 | #8c564b
%%metro line: l7 | L7 | #17becf

%%metro grid: tgt_sec | 0,0
%%metro grid: mid_sec | 1,0
%%metro grid: src_sec | 2,0

graph LR
    subgraph src_sec [Source]
        %%metro exit: left | l1, l2, l3, l4, l5, l6, l7
        s1[Start]
        s2[Out]
        s1 -->|l1,l2,l3,l4,l5,l6,l7| s2
    end
    subgraph mid_sec [Middle]
        m1[Mid]
        m2[MidOut]
        m1 -->|l1| m2
    end
    subgraph tgt_sec [Target]
        %%metro entry: left | l1, l2, l3, l4, l5, l6, l7
        t1[Process]
        t2[End]
        t1 -->|l1,l2,l3,l4,l5,l6,l7| t2
    end
    s2 -->|l1,l2,l3,l4,l5,l6,l7| t1

CLI command

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

Rendered map

Exit Corner Offset Dogleg

A passing line runs through a section on a per-line bundle offset, then exits and bypasses a higher row to climb to a far target. The onward run keeps the line's offset over the row-level traverse so it leaves the exit port straight, with the single level change a clean riser at the far gap rather than a one-offset-step jog at the exit corner.

Mermaid source

%% Issue #939: a flow-aligned exit whose in-section run carries a per-line
%% bundle offset must keep that offset on the onward run, not step back to the
%% bare port-marker row right after the exit corner. `mid` receives two lines
%% from `src`, so the passing line `l2` runs through `mid` on an offset track;
%% it then exits and bypasses `blocker` (a higher row) to climb to `dst`. The
%% onward run must leave the exit port straight (stay on l2's offset track over
%% the row-level traverse), with the single level change a clean riser at the
%% far gap -- no ~one-offset-step vertical jog at the exit corner.
%%metro title: Exit-corner offset dogleg (#939)
%%metro style: dark
%%metro line: l1 | L1 | #f5c542
%%metro line: l2 | L2 | #e63946
%%metro grid: src | 0,0
%%metro grid: mid | 1,1
%%metro grid: blocker | 2,0
%%metro grid: dst | 3,0

graph LR
    subgraph src [Src]
        a1[A1]
    end
    subgraph mid [Mid]
        m1[Mid]
    end
    subgraph blocker [Blocker]
        b1[Blk]
    end
    subgraph dst [Dst]
        d1[Dst]
    end

    a1 -->|l1| m1
    a1 -->|l2| m1
    m1 -->|l2| d1
    a1 -->|l1| b1
    b1 -->|l1| d1

CLI command

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

Rendered map

Convergent Offrow Exit Climb

A single-row long-read variant-calling map. The annotation section carries only snv and sv (the two highest-priority lines), reached through a bypass whose source re-based them onto low slots. Its two-line bundle anchors on its own trunk rather than inheriting the high global slots, so its markers sit on their rows and the run into reports stays level.

Mermaid source

%% Regression fixture for issue #941.  Single-row grid for the longread
%% variant-calling map.  The annotation section carries snvvcf+svvcf reached
%% through a bypass whose source re-based those lines, so its two-line bundle
%% must anchor on its own trunk (global slots 4,5 -> local 0,1) rather than
%% inheriting the high slots and pushing its markers ~18px below the row.
%%metro title: Long-read Variant Calling
%%metro style: dark
%%metro directional: true
%%metro files: fastq_in | FASTQ
%%metro files: bam_in | BAM
%%metro files: ubam_in | uBAM
%%metro line: ubam | uBAM | #0570b0
%%metro line: fastq | FASTQ | #2db572
%%metro line: bam | BAM | #f5c542
%%metro line: other | Other | #ff8c00
%%metro line: snvvcf | SNV VCF | #e63946
%%metro line: svvcf | SV VCF | #9d4edd
%%metro legend: tl
%%metro grid: preprocessing | 0,0
%%metro grid: small_variants | 1,0
%%metro grid: tr_calling | 1,1
%%metro grid: phasing | 2,0
%%metro grid: cnv_calling | 2,1
%%metro grid: structural_variants | 3,0
%%metro grid: jointcalling | 4,0
%%metro grid: annotation | 5,0
%%metro grid: reports | 6,0

graph LR
    subgraph preprocessing [Pre-processing]

        fastq_in[ ]
        bam_in[ ]
        ubam_in[ ]
        cat_fastq[cat FASTQ]
        samtools_merge[samtools\nmerge]
        minimap2_align[minimap2]
        samtools_sort_index[samtools\nsort/index]
        mosdepth[mosdepth]

        fastq_in -->|fastq| cat_fastq
        ubam_in -->|ubam| samtools_merge
        bam_in -->|bam| samtools_merge
        cat_fastq -->|fastq| minimap2_align
        samtools_merge -->|ubam| minimap2_align
        minimap2_align -->|bam| samtools_sort_index
        samtools_merge -->|bam| samtools_sort_index
        samtools_sort_index -->|bam| mosdepth
    end

    subgraph small_variants [Small variant calling]

        clair3[Clair3]
        deepvariant[Deepvariant]
    end

    subgraph cnv_calling [CNVs]

        ontspectre_cnvcaller[ont-spectre CNVCaller]
    end

    subgraph tr_calling [Repeats]

        longtr[LongTR]
        straglr[Straglr]
        trgt[TRGT]
    end

    subgraph phasing [Phasing]

        whatshap_phase[WhatsHap Phase]
        whatshap_haplotag[WhatsHap Haplotag]

        whatshap_phase -->|bam,snvvcf| whatshap_haplotag
    end

    subgraph structural_variants [Structural Variants]

        sniffles[Sniffles]
        cutesv[CuteSV]
        jasminesv_callers[Jasmine merge callers]

        sniffles -->|svvcf,bam| jasminesv_callers
        cutesv -->|svvcf,bam| jasminesv_callers
    end

    subgraph jointcalling [Joint Calling]

        jasminesv_samples[Jasmine merge samples]
        glnexus[GLNexus]
    end

    subgraph annotation [Annotation]

        vep[VEP]
        snpeff[SnpEff]
        annotsv[AnnotSV]
    end

    subgraph reports [Reports]

        geneyx[Geneyx]
        sv_report[SV Report]
    end


    %% Inter-section edges
    samtools_sort_index -->|bam| clair3
    samtools_sort_index -->|bam| deepvariant
    samtools_sort_index -->|bam| longtr
    samtools_sort_index -->|bam| straglr
    samtools_sort_index -->|bam| trgt

    mosdepth -->|other| ontspectre_cnvcaller

    straglr -->|other| geneyx

    clair3 -->|snvvcf| ontspectre_cnvcaller
    deepvariant -->|snvvcf| ontspectre_cnvcaller

    clair3 -->|bam,snvvcf| whatshap_phase
    deepvariant -->|bam,snvvcf| whatshap_phase

    clair3 -->|snvvcf| glnexus
    deepvariant -->|snvvcf| glnexus

    clair3 -->|snvvcf| vep
    deepvariant -->|snvvcf| vep

    whatshap_haplotag -->|bam| sniffles
    whatshap_haplotag -->|bam| cutesv
    whatshap_haplotag -->|bam| jasminesv_samples

    ontspectre_cnvcaller -->|other| geneyx

    sniffles -->|svvcf| jasminesv_samples
    sniffles -->|svvcf| vep
    sniffles -->|svvcf| snpeff
    sniffles -->|svvcf| annotsv
    sniffles -->|svvcf| geneyx

    cutesv -->|svvcf| jasminesv_samples
    cutesv -->|svvcf| vep
    cutesv -->|svvcf| snpeff
    cutesv -->|svvcf| annotsv
    cutesv -->|svvcf| geneyx

    jasminesv_callers -->|svvcf| jasminesv_samples
    jasminesv_callers -->|svvcf| vep
    jasminesv_callers -->|svvcf| snpeff
    jasminesv_callers -->|svvcf| annotsv
    jasminesv_callers -->|svvcf| geneyx
    jasminesv_callers -->|svvcf| sv_report

    snpeff -->|svvcf| sv_report
    annotsv -->|svvcf| sv_report

    glnexus -->|snvvcf| vep

CLI command

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

Rendered map

Fold Bypass Creep

A fold turns the calling section into a vertical bridge and a qc line forks around its file terminus into a separate downstream report section. Keeping the bypass feeds the bridge's height into the downstream section's placement, which settles one pass later, so the report section seats at its converged Y in both validated and unvalidated renders.

Mermaid source

%%metro title: Fold Bypass Creep
%%metro fold_threshold: 4
%%metro file: vcf_out | VCF
%%metro line: main | Main | #2db572
%%metro line: qc | QC | #0570b0

graph LR
    subgraph prep [Prep]
        in0[ ]
        align[Align]
        in0 -->|main,qc| align
    end
    subgraph calling [Calling]
        caller1[Caller A]
        caller2[Caller B]
        stats[Stats]
        collate[ ]
        vcf_out[ ]
        caller1 -->|main| stats
        caller2 -->|main| stats
        stats -->|main| collate
        collate -->|main| vcf_out
    end
    subgraph report [Report]
        mqc[MultiQC]
    end
    align -->|main| caller1
    align -->|main| caller2
    stats -->|qc| mqc
    align -->|qc| mqc

CLI command

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

Rendered map

Fold Bypass Creep Tight

The tight variant of the fold bypass, where the file terminus sits one row below the forking station, so the qc bypass V seats on the trailing row. The folded section's perpendicular exit corridor clears the V by a full station-flat length, so the bypass run-out reads as a visible flat rather than collapsing onto the curve apex.

Mermaid source

%%metro title: Fold Bypass Creep (tight)
%%metro fold_threshold: 4
%%metro file: vcf_out | VCF
%%metro line: main | Main | #2db572
%%metro line: qc | QC | #0570b0

graph LR
    subgraph prep [Prep]
        in0[ ]
        align[Align]
        in0 -->|main,qc| align
    end
    subgraph calling [Calling]
        caller1[Caller A]
        caller2[Caller B]
        stats[Stats]
        vcf_out[ ]
        caller1 -->|main| stats
        caller2 -->|main| stats
        stats -->|main| vcf_out
    end
    subgraph report [Report]
        mqc[MultiQC]
    end
    align -->|main| caller1
    align -->|main| caller2
    stats -->|qc| mqc
    align -->|qc| mqc

CLI command

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

Rendered map

Merge & Convergence

Merge Offrow Continuation

A perpendicular feeder re-slots at a multi-feeder merge port, and the single re-joined line leaves the merge row before reaching its consumer one row up, so the bundle-offset walk stops at the off-row exit rather than carrying the slot off the row.

Mermaid source

%%metro title: Off-Row Merge Continuation
%%metro style: dark
%%metro line: trunk | Trunk | #2db572
%%metro line: bypass | Bypass | #e63946

%%metro grid: above_src | 0,0
%%metro grid: horiz_src | 0,1
%%metro grid: sink | 1,1
%%metro grid: out | 2,0

graph LR
    subgraph above_src [Above Source]
        %%metro exit: right | bypass
        a1[Start A]
        a2[Prep A]
        a1 -->|bypass| a2
    end

    subgraph horiz_src [Horizontal Source]
        %%metro exit: right | trunk
        h1[Start B]
        h2[Prep B]
        h1 -->|trunk| h2
    end

    subgraph sink [Sink]
        %%metro entry: left | trunk,bypass
        %%metro exit: right | trunk
        s1[Merge]
        s2[Combine]
        s1 -->|trunk,bypass| s2
    end

    subgraph out [Output]
        o1[Report]
    end

    a2 -->|bypass| s1
    h2 -->|trunk| s1
    s2 -->|trunk| o1

CLI command

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

Rendered map

Junction Entry Reversed Fold

A two-line bundle exits a TB section's RIGHT side, wraps into a Source section, then fans out at a junction into two same-row destinations. The bundle order is carried concentrically through the reversal corners so the lines never cross at a station, and the fan-out peels off cleanly (issue #760).

Mermaid source

%%metro title: Junction Entry Reversed Fold
%%metro style: dark
%%metro line: alpha | Alpha | #e63946
%%metro line: beta | Beta | #2db572
%%metro grid: tb | 0,0
%%metro grid: src | 1,0
%%metro grid: dst_a | 2,0
%%metro grid: dst_b | 3,0

graph LR
    subgraph tb [Bridge]
        %%metro direction: TB
        %%metro exit: right | alpha,beta
        tb1[Mark]
        tb2[Recal]
        tb1 -->|alpha,beta| tb2
    end

    subgraph src [Source]
        %%metro entry: left | alpha,beta
        %%metro exit: right | alpha,beta
        s_hub[Hub]
    end

    subgraph dst_a [Dest Alpha]
        %%metro entry: left | alpha
        da1[Process A]
        da2[Output A]
        da1 -->|alpha| da2
    end

    subgraph dst_b [Dest Beta]
        %%metro entry: left | beta
        db1[Process B]
        db2[Output B]
        db1 -->|beta| db2
    end

    tb2 -->|alpha,beta| s_hub
    s_hub -->|alpha| da1
    s_hub -->|beta| db1

CLI command

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

Rendered map

Convergence Stacked Sink

A leaf sink that would otherwise sit alone in the spine band migrates into the convergence return row (no grid-cell collision).

Mermaid source

%%metro title: Convergence Stacked Sink
%%metro style: dark
%%metro line: main | Main | #0570b0

graph LR
    subgraph prep [Prep]
        p1[Input]
        p2[Output]
        p1 -->|main| p2
    end

    subgraph aux [Aux Input]
        x1[Load]
        x2[Index]
        x1 -->|main| x2
    end

    subgraph align [Align]
        a1[Map]
        a2[Sort]
        a1 -->|main| a2
    end

    subgraph repeats [Repeats]
        r1[Detect]
        r2[Genotype]
        r1 -->|main| r2
    end

    subgraph dedup [Dedup]
        d1[Mark]
        d2[Recal]
        d1 -->|main| d2
    end

    subgraph merge_pt [Merge]
        g1[Combine]
        g2[Refine]
        g1 -->|main| g2
    end

    subgraph report [Report]
        rp1[Summarise]
        rp2[Publish]
        rp1 -->|main| rp2
    end

    p2 -->|main| a1
    x2 -->|main| r1
    a2 -->|main| d1
    d2 -->|main| g1
    r2 -->|main| g1
    p2 -->|main| g1
    g2 -->|main| rp1

CLI command

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

Rendered map

Convergence Sink Above

An input section sits above the shared sink it feeds, while its line is declared last. The sink's entry bundle is slotted by feeder approach (the feeder whose source sits highest takes the topmost lane) rather than by declaration order, so the line runs straight into the port instead of dropping down across its bundle-mate.

Mermaid source

%%metro title: Convergence Sink Above
%%metro style: dark
%%metro compact_offsets: true
%%metro line: lower | Lower | #e63946
%%metro line: upper | Upper | #0570b0
%%metro grid: up_in | 0,0
%%metro grid: low_in | 0,1
%%metro grid: sink | 1,1

graph LR
    subgraph up_in [Upper Input]
        u1[Load]
        u2[Prep]
        u1 -->|upper| u2
    end
    subgraph low_in [Lower Input]
        d1[Load]
        d2[Prep]
        d1 -->|lower| d2
    end
    subgraph sink [Merge]
        s1[Collect]
        s2[Report]
        s1 -->|lower,upper| s2
    end
    d2 -->|lower| s1
    u2 -->|upper| s1

CLI command

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

Rendered map

Terminus Join

Two lines converge on a single file-icon terminus in a sectionless flat graph, so the join lands directly on the terminus rather than a synthesised convergence junction.

Mermaid source

%%metro title: Terminus Join
%%metro style: dark
%%metro line: l1 | Line 1 | #e63946
%%metro line: l2 | Line 2 | #2db572
%%metro file: sink_out | OUT | Results

graph LR
    src_a[Process A]
    src_b[Process B]
    sink_out[ ]
    src_a -->|l1| sink_out
    src_b -->|l2| sink_out

CLI command

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

Rendered map

Merge Port Above Approach

A line descending into a multi-feeder merge port from a section above keeps the above-trunk slot all the way to the output, so its riser joins the bundle without crossing the trunk on the outgoing run (issue #704).

Mermaid source

%%metro title: Above Approach Merge
%%metro style: dark
%%metro line: trunk | Trunk | #2db572
%%metro line: bypass | Bypass | #e63946

%%metro grid: above_src | 0,0
%%metro grid: horiz_src | 0,1
%%metro grid: sink | 1,1
%%metro grid: out | 2,1

graph LR
    subgraph above_src [Above Source]
        %%metro exit: right | bypass
        a1[Start A]
        a2[Prep A]
        a1 -->|bypass| a2
    end

    subgraph horiz_src [Horizontal Source]
        %%metro exit: right | trunk
        h1[Start B]
        h2[Prep B]
        h1 -->|trunk| h2
    end

    subgraph sink [Sink]
        %%metro entry: left | trunk,bypass
        %%metro exit: right | trunk,bypass
        s1[Merge]
        s2[Combine]
        s1 -->|trunk,bypass| s2
    end

    subgraph out [Output]
        o1[Report]
    end

    a2 -->|bypass| s1
    h2 -->|trunk| s1
    s2 -->|trunk,bypass| o1

CLI command

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

Rendered map

Junction Entry Collision

A three-line fan-out where one line continues straight to its own destination while the other two branch away: the straight line keeps a constant bundle slot across the source exit so its trunk stays horizontal (issue #704).

Mermaid source

%%metro title: Junction Entry Collision Skip
%%metro style: dark
%%metro line_order: span
%%metro line: beta | Beta | #2db572
%%metro line: alpha | Alpha | #e63946
%%metro line: gamma | Gamma | #0570b0

%%metro grid: pre | 0,0
%%metro grid: src | 1,0
%%metro grid: dst_a | 2,0
%%metro grid: dst_bg | 3,0

graph LR
    subgraph pre [Pre]
        pre1[Start]
        pre2[Prep]
        pre1 -->|alpha,beta,gamma| pre2
    end

    subgraph src [Source]
        %%metro exit: right | alpha,beta,gamma
        s_a[Alpha Tool]
        s_b[Beta Tool]
        s_g[Gamma Tool]
    end

    subgraph dst_a [Dest Alpha]
        %%metro entry: left | alpha
        da1[Output A]
    end

    subgraph dst_bg [Dest Beta+Gamma]
        %%metro entry: left | beta,gamma
        dbg1[Output B+G]
        dbg2[Report]
        dbg1 -->|beta,gamma| dbg2
    end

    pre2 -->|alpha| s_a
    pre2 -->|beta| s_b
    pre2 -->|gamma| s_g
    s_a -->|alpha| da1
    s_b -->|beta| dbg1
    s_g -->|gamma| dbg1

CLI command

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

Rendered map

Junction Entry Align

A two-line bundle whose order is preserved across the junction-to-entry-port boundary, so the straight-through line stays horizontal instead of slanting to swap slots (issue #704).

Mermaid source

%%metro title: Junction Entry Port Align
%%metro style: dark
%%metro line_order: span
%%metro line: alpha | Alpha | #e63946
%%metro line: beta | Beta | #2db572

%%metro grid: pre | 0,0
%%metro grid: src | 1,0
%%metro grid: dst_a | 2,0
%%metro grid: dst_b | 3,0
%%metro grid: beta_extra_1 | 0,1
%%metro grid: beta_extra_2 | 1,1

graph LR
    subgraph pre [Pre]
        pre1[Start]
        pre2[Prep]
        pre1 -->|alpha,beta| pre2
    end

    subgraph beta_extra_1 [Beta Extra 1]
        be1_1[Step]
        be1_2[Step 2]
        be1_1 -->|beta| be1_2
    end

    subgraph beta_extra_2 [Beta Extra 2]
        be2_1[Step]
        be2_2[Step 2]
        be2_1 -->|beta| be2_2
    end

    subgraph src [Source]
        %%metro exit: right | alpha,beta
        s_a[Tool Alpha]
        s_b[Tool Beta]
    end

    subgraph dst_a [Dest Alpha]
        %%metro entry: left | alpha
        da1[Process A]
        da2[Output A]
        da1 -->|alpha| da2
    end

    subgraph dst_b [Dest Beta]
        %%metro entry: left | beta
        db1[Process B]
        db2[Output B]
        db1 -->|beta| db2
    end

    pre2 -->|alpha| s_a
    pre2 -->|beta| s_b
    pre2 -->|beta| be1_1
    be1_2 -->|beta| be2_1
    s_a -->|alpha| da1
    s_b -->|beta| db1

CLI command

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

Rendered map

Merge Trunk Out Of Range Section

Two same-row sources merge into one sink past an intervening section while another row's section sits outside the merge column range, so the merge trunk keeps its same-row bypass channel rather than crossing below the out-of-range section.

Mermaid source

%%metro title: Merge Trunk Out-of-Range Section
%%metro style: dark
%%metro line: main | Main | #2db572
%%metro grid: src_far | 0, 0
%%metro grid: mid | 1, 0
%%metro grid: src_near | 2, 0
%%metro grid: sink | 3, 0
%%metro grid: extra | 4, 0
%%metro grid: other | 5, 1

graph LR
    subgraph src_far [Source Far]
        %%metro exit: right | main
        far1[Far]
    end

    subgraph mid [Mid]
        %%metro entry: left | main
        %%metro exit: right | main
        m1[Mid Step]
    end

    subgraph src_near [Source Near]
        %%metro entry: left | main
        %%metro exit: right | main
        near1[Near]
    end

    subgraph sink [Sink]
        %%metro entry: left | main
        merge[Merge]
        report[Report]
        merge -->|main| report
    end

    subgraph extra [Extra]
        %%metro entry: left | main
        e1[Extra Step]
    end

    subgraph other [Other Row]
        %%metro entry: top | main
        o1[Other]
    end

    m1 -->|main| near1
    far1 -->|main| merge
    near1 -->|main| merge
    far1 -->|main| e1
    near1 -->|main| e1
    e1 -->|main| o1

CLI command

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

Rendered map

Merge Trunk Over Low Section

A same-row merge trunk bypasses past a tall intervening section while a lower-row section sits within the merge column range. The inter-row gap clears the lower section's header, so the trunk (and its branches) route through that gap rather than diving below the whole canvas.

Mermaid source

%%metro title: Merge Trunk Over Low Section
%%metro style: dark
%%metro line: flow | Flow | #0570b0
%%metro line: side | Side | #2db572

%%metro grid: ingest | 0,0
%%metro grid: tall | 1,0
%%metro grid: proc2 | 2,0
%%metro grid: collect | 3,0
%%metro grid: sub | 2,1

graph LR
    subgraph ingest [Ingest]
        i1[Read]
        i2[Split]
        i1 -->|flow,side| i2
    end

    subgraph tall [Tall]
        ta[Branch]
        tb1[Path A]
        tb2[Path B]
        tb3[Path C]
        ta -->|flow| tb1
        ta -->|flow| tb2
        ta -->|flow| tb3
    end

    subgraph proc2 [Proc 2]
        q1[Step]
    end

    subgraph collect [Collect]
        c1[Gather]
        c2[Report]
        c1 -->|flow| c2
    end

    subgraph sub [Sub]
        d1[Aux]
        d2[Done]
        d1 -->|side| d2
    end

    i2 -->|flow| ta
    i2 -->|flow| c1
    tb1 -->|flow| q1
    tb1 -->|flow| c1
    q1 -->|flow| c1
    i2 -->|side| d1

CLI command

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

Rendered map

Merge Bottom Row Bypass

A merge whose entry sits in the bottommost grid row: the trunk's inter-row bypass routes in the cramped gap above that row. Placement reserves the gap so the channel clears the upper row's section boxes instead of grazing them.

Mermaid source

%%metro title: Bottommost-Row Merge Inter-Row Bypass
%%metro style: dark
%%metro line: a | A | #e63946
%%metro line: b | B | #0570b0
%%metro grid: src_fanA | 2,0
%%metro grid: src_fanB | 2,1
%%metro grid: side_a | 3,0
%%metro grid: middle | 1,1
%%metro grid: target | 0,2

graph LR
    subgraph src_fanA [Fan Source A]
        fsa1[In]
        fsa2[Out]
        fsa1 -->|a| fsa2
    end
    subgraph src_fanB [Fan Source B]
        fsb1[In]
        fsb2[Out]
        fsb1 -->|a| fsb2
    end
    subgraph side_a [Side]
        %%metro entry: left | a
        sia1[Side]
        sia2[Out]
        sia1 -->|a| sia2
    end
    subgraph middle [Middle]
        m1[Process]
        m2[Out]
        m1 -->|b| m2
    end
    subgraph target [Target]
        %%metro direction: RL
        %%metro entry: right | a
        t1[Process]
        t2[Out]
        t1 -->|a| t2
    end
    fsa2 -->|a| t1
    fsa2 -->|a| sia1
    fsb2 -->|a| t1
    fsb2 -->|a| sia1

CLI command

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

Rendered map

Merge Pullaway

One line converges on a merge from two stacked rows of the same column; the cross-row feeder drops onto the trunk's pull-away bypass channel and the two travel as a single stroke into the entry.

Mermaid source

%%metro title: Merge trunk pull-away cross-row sibling
%%metro style: dark
%%metro line: main | Main | #0570b0
%%metro grid: wide_src | 0,0
%%metro grid: obstacle | 1,0
%%metro grid: sibling_sec | 0,1
%%metro grid: side_dst | 2,1
%%metro grid: target | 2,0

graph LR
    subgraph wide_src [Wide Source]
        w1[Start]
        w2[Out]
        w1 -->|main| w2
    end
    subgraph obstacle [Obstacle]
        o1[Block]
        o2[Pass]
        o1 -->|main| o2
    end
    subgraph sibling_sec [Sibling]
        s1[Step]
        s2[Done]
        s1 -->|main| s2
    end
    subgraph side_dst [Side Dest]
        sd1[Side]
        sd2[Out]
        sd1 -->|main| sd2
    end
    subgraph target [Target]
        %%metro entry: left | main
        t1[Merge]
        t2[Report]
        t1 -->|main| t2
    end
    w2 -->|main| o1
    w2 -->|main| t1
    s2 -->|main| sd1
    s2 -->|main| t1

CLI command

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

Rendered map

Merge Right Entry

One line converges on a RIGHT entry whose consumer is the sink's flow-start station: the sink flows right-to-left so the merge arrives beside its consumer, and the trunk loops under the sink onto that channel rather than slicing across the box to the far station (#885).

Mermaid source

%%metro title: Merge Right Entry Cross Row
%%metro style: dark
%%metro line: main | Main | #0570b0
%%metro grid: sink | 0,0
%%metro grid: source | 2,1
%%metro grid: extra | 4,1
%%metro grid: step_a | 6,1

graph LR
    subgraph sink [Sink]
        %%metro entry: right | main
        t1[Collect]
        t2[Report]
        t1 -->|main| t2
    end
    subgraph source [Source]
        s1[Produce]
        s2[Prepare]
        s1 -->|main| s2
    end
    subgraph extra [Extra]
        e1[Extra]
        e2[Extra Out]
        e1 -->|main| e2
    end
    subgraph step_a [Step A]
        a1[Process A]
        a2[Out A]
        a1 -->|main| a2
    end
    s2 -->|main| e1
    s2 -->|main| t1
    e2 -->|main| a1
    e2 -->|main| t1
    a2 -->|main| t1

CLI command

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

Rendered map

Peeloff Riser Respace

Four lines from two sources ride one shared bypass trunk and rise into a common destination entry port, where the trunk-Y order and the entry-port slot order disagree. Each source bundle keeps its declaration order at the peel-off corner instead of inverting (issue #695).

Mermaid source

%%metro title: Peel-off Riser Respace
%%metro style: dark
%%metro line: l1 | Line 1 | #e63946
%%metro line: l2 | Line 2 | #2db572
%%metro line: l3 | Line 3 | #0570b0
%%metro line: l4 | Line 4 | #f5c542
%%metro grid: src_a | 0,0
%%metro grid: src_b | 1,0
%%metro grid: mid | 2,0
%%metro grid: dst | 3,0

graph LR
    subgraph src_a [Source A]
        %%metro exit: right | l1,l2
        sa_in[Input A]
        sa_out[Output A]
        sa_in -->|l1,l2| sa_out
    end

    subgraph src_b [Source B]
        %%metro entry: left | l3,l4
        %%metro exit: right | l3,l4
        sb_in[Input B]
        sb_out[Output B]
        sb_in -->|l3,l4| sb_out
    end

    subgraph mid [Mid]
        m1[Mid Process]
    end

    subgraph dst [Destination]
        %%metro entry: left | l1,l2,l3,l4
        d1[Process D1]
        d2[Process D2]
        d1 -->|l1,l2,l3,l4| d2
    end

    sa_out -->|l1,l2| d1
    sb_out -->|l3,l4| d1

CLI command

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

Rendered map

Peeloff Extra Line Consumer

Same peel-off topology as peeloff_riser_respace but the destination section also carries an extra internal branch (l5). The riser reorder must still fire and keep the bundle crossing-free at the shared entry port regardless of extra lines in the consumer section (issue #751).

Mermaid source

%%metro title: Peel-off Extra Line Consumer
%%metro style: dark
%%metro line: l1 | Line 1 | #e63946
%%metro line: l2 | Line 2 | #2db572
%%metro line: l3 | Line 3 | #0570b0
%%metro line: l4 | Line 4 | #f5c542
%%metro line: l5 | Line 5 | #9b59b6
%%metro grid: src_a | 0,0
%%metro grid: src_b | 1,0
%%metro grid: mid | 2,0
%%metro grid: dst | 3,0

graph LR
    subgraph src_a [Source A]
        %%metro exit: right | l1,l2
        sa_in[Input A]
        sa_out[Output A]
        sa_in -->|l1,l2| sa_out
    end

    subgraph src_b [Source B]
        %%metro entry: left | l3,l4
        %%metro exit: right | l3,l4
        sb_in[Input B]
        sb_out[Output B]
        sb_in -->|l3,l4| sb_out
    end

    subgraph mid [Mid]
        m1[Mid Process]
    end

    subgraph dst [Destination]
        %%metro entry: left | l1,l2,l3,l4
        d1[Process D1]
        d2[Process D2]
        d3[Process D3]
        d1 -->|l1,l2,l3,l4| d2
        d2 -->|l5| d3
    end

    sa_out -->|l1,l2| d1
    sb_out -->|l3,l4| d1

CLI command

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

Rendered map

Merge Leftmost Sink Branch

A leftward merge whose trunk reaches a leftmost-column sink's LEFT entry: the trunk wraps to rise on the box's far (left) side, with the branch feeders converging on its shared channel, rather than crossing the sink interior to the far-side port.

Mermaid source

%%metro title: Merge Leftmost Sink Branch
%%metro style: dark
%%metro line: a | A | #e63946

%%metro grid: blocker | 1,0
%%metro grid: step_a | 3,0
%%metro grid: step_b | 5,0
%%metro grid: extra | 6,0
%%metro grid: sink | 0,1

graph LR
    subgraph blocker [Blocker]
        bl1[Block Start]
        bl2[Block End]
        bl1 -->|a| bl2
    end

    subgraph step_a [Step A]
        a1[Process A]
        a2[Out A]
        a1 -->|a| a2
    end

    subgraph step_b [Step B]
        b1[Process B]
        b2[Out B]
        b1 -->|a| b2
    end

    subgraph extra [Extra]
        e1[Extra]
        e2[Extra Out]
        e1 -->|a| e2
    end

    subgraph sink [Sink]
        t1[Collect]
        t2[Report]
        t1 -->|a| t2
    end

    bl2 -->|a| a1
    a2 -->|a| b1
    a2 -->|a| t1
    b2 -->|a| e1
    b2 -->|a| t1

CLI command

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

Rendered map

Merge Around Below Leftmost

Two sources merging into a leftmost-column LEFT entry: the trunk routes around the target's left side to enter from outside while the second merge target is reached in-row.

Mermaid source

%%metro title: Merge Around Below Leftmost
%%metro style: nfcore
%%metro line: a | A | #e63946
%%metro grid: src1  | 1,0
%%metro grid: src2  | 2,0
%%metro grid: extra | 3,0
%%metro grid: tgt   | 0,1

graph LR
    subgraph src1 [Source 1]
        a1[Step A]
        a2[Out A]
        a1 -->|a| a2
    end

    subgraph src2 [Source 2]
        b1[Step B]
        b2[Out B]
        b1 -->|a| b2
    end

    subgraph extra [Extra]
        %%metro entry: left | a
        e1[Extra Step]
        e2[Extra Out]
        e1 -->|a| e2
    end

    subgraph tgt [Target]
        %%metro entry: left | a
        t1[Combine]
        t2[Result]
        t1 -->|a| t2
    end

    a2 -->|a| e1
    a2 -->|a| t1
    b2 -->|a| e1
    b2 -->|a| t1

CLI command

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

Rendered map

Post Convergence Trunk

Two stacked inputs converge on a station inside one LR section. The merge station's single linear successor continues flat on the merge row rather than dropping back onto one of the incoming branch rows, so the post-merge trunk runs straight instead of zigzagging.

Mermaid source

%%metro title: Post-convergence trunk
%%metro line: fastq | FASTQ | #2db572
%%metro line: ubam | uBAM | #0570b0
%%metro line: bam | BAM | #f5c542

graph LR
    subgraph prep [Prep]
        fq[FQ]
        ub[UB]
        mm[minimap2]
        st[samtools]
        fq -->|fastq| mm
        ub -->|ubam| mm
        mm -->|bam| st
    end

CLI command

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

Rendered map

Junction Fanout Convergence

Three lines converge into one joint-calling entry port: two bypass the intervening sections and climb risers into the port while the third joins flat from the adjacent column. The flat shallow feeder takes the port-near slot on top of the climbing pair so the bundle turns into the port concentrically, instead of the flat line weaving across the risers at the corner.

Mermaid source

%% Three lines converge into one LEFT entry port on a single-row grid: a and b
%% bypass the intervening sections and climb risers into the port, while c joins
%% flat from the adjacent column. The shallow feeder c must nest port-near on
%% top of the climbing pair so the bundle turns concentrically rather than
%% weaving c across the risers at the corner (#940).
%%metro title: Junction Fan-out Convergence
%%metro style: dark
%%metro line: a | Line A | #e63946
%%metro line: b | Line B | #f5c542
%%metro line: c | Line C | #9d4edd
%%metro grid: stepA | 0,0
%%metro grid: stepB | 1,0
%%metro grid: stepC | 2,0
%%metro grid: joint | 3,0

graph LR
    subgraph stepA [Caller A]
        sa[Call A]
    end
    subgraph stepB [Caller B]
        sb[Call B]
    end
    subgraph stepC [Caller C]
        sc[Call C]
    end
    subgraph joint [Joint Calling]
        merge[Merge]
        collect[Collect]
    end

    sa -->|a| merge
    sb -->|b| merge
    sc -->|c| merge
    merge -->|a,b,c| collect

CLI command

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

Rendered map

Aligner Row Pinned Continuation

Three sibling aligners feed one dedup hub that lands on the lead aligner's row, while one aligner's line continues on a track pinned to the section bottom by hidden continuation stations. The aligners stack on consecutive grid rows instead of the low-line aligner being dragged down to crowd its neighbour and strand the middle row (#1071).

Mermaid source

%%metro title: Aligner row vs pinned continuation
%%metro line: star_rsem | STAR/RSEM | #0570b0
%%metro line: star_salmon | STAR/Salmon | #2db572
%%metro line: hisat2 | HISAT2 | #f5c542
%%metro line: bowtie2_salmon | Bowtie2/Salmon | #ff8c00

graph LR
    subgraph preproc [Pre-processing]
        %%metro exit: right | star_salmon, star_rsem, hisat2, bowtie2_salmon
        fastqc_filtered[FastQC]
    end

    subgraph genome_align [Genome alignment & quantification]
        %%metro entry: left | star_salmon, star_rsem, hisat2, bowtie2_salmon
        %%metro exit: right | star_salmon, star_rsem
        %%metro exit: right | hisat2
        star[STAR]
        hisat2_align[HISAT2]
        bowtie2_align[Bowtie2]
        rsem[RSEM]
        salmon_quant[Salmon]
        umi_tools_dedup[UMI-tools Dedup]
        tximport_ga[tximport]
        summarized_exp_ga[Sum. Exp.]
        multiqc_bowtie2[MultiQC]
        report_bowtie2[ ]
        _h1[hidden]
        _h2[hidden]
        _h3[hidden]

        star -->|star_rsem,star_salmon| umi_tools_dedup
        hisat2_align -->|hisat2| umi_tools_dedup
        bowtie2_align -->|bowtie2_salmon| umi_tools_dedup
        umi_tools_dedup -->|star_rsem| rsem
        umi_tools_dedup -->|star_salmon| salmon_quant
        umi_tools_dedup -->|hisat2| _h1
        _h1 -->|hisat2| _h2
        _h2 -->|hisat2| _h3
        salmon_quant -->|star_salmon| tximport_ga
        rsem -->|star_rsem| tximport_ga
        tximport_ga -->|star_salmon,star_rsem| summarized_exp_ga
        umi_tools_dedup -->|bowtie2_salmon| salmon_quant
        salmon_quant -->|bowtie2_salmon| multiqc_bowtie2
        multiqc_bowtie2 -->|bowtie2_salmon| report_bowtie2
    end

    subgraph postproc [Post-processing]
        %%metro direction: TB
        %%metro entry: left | star_salmon, star_rsem, hisat2
        samtools[SAMtools]
        picard[Picard]

        samtools -->|star_salmon,star_rsem,hisat2| picard
    end

    fastqc_filtered -->|star_salmon,star_rsem| star
    fastqc_filtered -->|hisat2| hisat2_align
    fastqc_filtered -->|bowtie2_salmon| bowtie2_align
    summarized_exp_ga -->|star_salmon,star_rsem| samtools
    _h3 -->|hisat2| samtools

CLI command

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

Rendered map

Fanin Distant Terminus

Two sibling methods feed one report icon while a third continues through a longer ORF chain that pushes the report to the far end of the section. The siblings converge at a local junction one column on and a single trunk carries the merged line to the report, instead of the two legs bowing out and running parallel the whole way to the distant merge (issue #1296).

Mermaid source

%%metro title: Fan-in to a distant terminus
%%metro file: report | HTML | Report
%%metro line: a | Line A | #e6007e

graph LR
    subgraph s1 [Translational efficiency]
        prep[Prep]
        anota[anota2seq]
        delta[deltaTE]
        dotseq[DOTSeq]
        orf_quant[ORFquant]
        orf_test[ORFtest]
        prep -->|a| anota
        prep -->|a| delta
        prep -->|a| dotseq
        dotseq -->|a| orf_quant
        orf_quant -->|a| orf_test
        anota -->|a| report
        delta -->|a| report
        orf_test -->|a| report
    end

CLI command

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

Rendered map

Off-track & Rails

Off Track Convergence

Multiple off-track file inputs converging on a single consumer. The trunk stays horizontal while the inputs stack above the consumer column.

Mermaid source

%%metro title: Off-Track Convergence
%%metro style: dark
%%metro line: main | Main | #2db572
%%metro file: ref_in | FASTA | Reference
%%metro file: gtf_in | GTF | Annotation
%%metro file: vcf_in | VCF | Known Variants
%%metro file: bed_in | BED | Targets
%%metro off_track: ref_in, gtf_in, vcf_in, bed_in

graph LR
    subgraph input [Input]
        reads[Reads]
        prep[Prepare]
        reads -->|main| prep
    end

    subgraph process [Process]
        ref_in[ ]
        gtf_in[ ]
        vcf_in[ ]
        bed_in[ ]
        align[Align]
        annotate[Annotate]

        ref_in -->|main| align
        gtf_in -->|main| align
        vcf_in -->|main| align
        bed_in -->|main| align
        align -->|main| annotate
    end

    subgraph output [Output]
        report[Report]
    end

    prep -->|main| align
    annotate -->|main| report

CLI command

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

Rendered map

Off Track Convergence Multiline

A multi-line bundle enters a section and converges on a deep first station that also consumes off-track file inputs. The consumer stays on the section trunk, level with its continuation, rather than being dragged to the section floor (issue #650).

Mermaid source

%%metro title: Off-Track Convergence Multiline
%%metro style: dark
%%metro line: dna | DNA | #2db572
%%metro line: rna | RNA | #e63946
%%metro line: qc | QC | #f4a261
%%metro file: ref_in | FASTA | Reference
%%metro file: gtf_in | GTF | Annotation
%%metro off_track: ref_in, gtf_in

graph LR
    subgraph input [Input]
        reads[Reads]
        prep[Prepare]
        reads -->|dna,rna,qc| prep
    end

    subgraph process [Process]
        ref_in[ ]
        gtf_in[ ]
        align[Align]
        sort[Sort]
        index[Index]

        ref_in -->|dna,rna| align
        gtf_in -->|rna| align
        align -->|dna,rna,qc| sort
        sort -->|dna,rna,qc| index
    end

    subgraph output [Output]
        report[Report]
    end

    prep -->|dna,rna,qc| align
    index -->|dna,rna,qc| report

CLI command

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

Rendered map

Off Track Input Above Consumer

A section whose mid-trunk station consumes an off-track input while a neighbouring station feeds an off-track output. The input hugs one row above its consumer instead of towering an extra slot up because it shares an anchor with the differently-columned output (issue #651).

Mermaid source

%%metro title: Long-read Methylation & Variant Atlas
%%metro style: dark
%%metro line: dna | DNA variants | #2db572
%%metro line: rna | RNA expression | #e63946
%%metro line: qc | QC stream | #f4a261

%%metro file: ref_fa | FASTA | Reference
%%metro file: gtf_in | GTF | Annotation
%%metro file: cpg_bed | BED | CpG islands
%%metro off_track: ref_fa, gtf_in, cpg_bed

%%metro file: raw_bam | BAM | Aligned
%%metro file: meth_bw | bigWig | Methylation
%%metro off_track: raw_bam, meth_bw

graph LR
    subgraph intake [Intake & Basecall]
        in_pod5[POD5]
        in_basecall[Basecall]
        in_demux[Demux]
        in_qc[ReadQC]

        in_pod5 -->|dna,rna,qc| in_basecall
        in_basecall -->|dna,rna,qc| in_demux
        in_demux -->|dna,rna,qc| in_qc
    end

    subgraph align [Alignment]
        ref_fa[ ]
        gtf_in[ ]
        al_minimap[minimap2]
        al_sort[Sort]
        al_index[Index]
        raw_bam[ ]

        ref_fa -->|dna,rna| al_minimap
        gtf_in -->|rna| al_minimap
        al_minimap -->|dna,rna,qc| al_sort
        al_sort -->|dna,rna,qc| al_index
        al_sort -->|dna| raw_bam
    end

    subgraph methcall [Methylation Calling]
        mc_modkit[modkit]
        mc_pileup[Pileup]
        mc_dmr[DMR]
        cpg_bed[ ]
        meth_bw[ ]

        cpg_bed -->|dna| mc_pileup
        mc_modkit -->|dna| mc_pileup
        mc_pileup -->|dna| mc_dmr
        mc_pileup -->|dna| meth_bw
    end

    subgraph variants [Variant Calling]
        vc_clair[Clair3]
        vc_phase[Phase]
        vc_filter[Filter]

        vc_clair -->|dna| vc_phase
        vc_phase -->|dna| vc_filter
    end

    subgraph expr [Expression]
        ex_isoquant[IsoQuant]
        ex_count[Count]
        ex_norm[Normalize]

        ex_isoquant -->|rna| ex_count
        ex_count -->|rna| ex_norm
    end

    subgraph fusion [Fusion Detection]
        fu_jaffal[JAFFAL]
        fu_annotate[Annotate]

        fu_jaffal -->|rna| fu_annotate
    end

    subgraph merge [Merge & Annotate]
        mg_collect[Collect]
        mg_vep[VEP]
        mg_classify[Classify]

        mg_collect -->|dna,rna| mg_vep
        mg_vep -->|dna,rna| mg_classify
    end

    subgraph report [Report]
        rp_aggregate[Aggregate]
        rp_multiqc[MultiQC]
        rp_final[Report]

        rp_aggregate -->|dna,rna,qc| rp_multiqc
        rp_multiqc -->|dna,rna,qc| rp_final
    end

    in_qc -->|dna,rna,qc| al_minimap
    al_index -->|dna| mc_modkit
    al_index -->|dna| vc_clair
    al_index -->|rna| ex_isoquant
    al_index -->|rna| fu_jaffal
    al_index -->|qc| rp_aggregate
    mc_dmr -->|dna| mg_collect
    vc_filter -->|dna| mg_collect
    ex_norm -->|rna| mg_collect
    fu_annotate -->|rna| mg_collect
    mg_classify -->|dna,rna| rp_aggregate

CLI command

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

Rendered map

Off Track Terminal Noop

A station marked off_track whose only continuation is an inter-section edge to the next section, with no in-section successor. It renders inline on the trunk rather than lifting into a bump that immediately drops back down to reach the exit port (issue #1295).

Mermaid source

%%metro title: Off-track Terminal Has Nothing to Protect
%%metro style: dark
%%metro line: a | Line A | #2db572

%%metro file: out1 | GTF | Output
%%metro off_track: out1

graph LR
    subgraph s1 [S1]
        %%metro exit: right | a
        n1[N1]
        n2[N2]
        n1 -->|a| n2
        n2 -->|a| out1
    end

    subgraph s2 [S2]
        %%metro entry: left | a
        m1[M1]
        out1 -->|a| m1
    end

CLI command

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

Rendered map

Tb Off Track Output Row

A `direction: TB` section whose trunk stations feed off-track outputs. Each output hangs off its producer via an S -- a flow-axis lead down the trunk, a diagonal, then a flat tail into the icon -- on the side opposite the beside-trunk labels, the rotation of the LR off-track idiom, rather than leaving perpendicular or dropping onto the label side (issue #1384).

Mermaid source

%%metro title: TB off-track output row
%% Regression for #1384: in a `direction: TB` section an off-track output
%% (producer-fed sink) hangs off its producer via an S -- a flow-axis lead down
%% the trunk, a diagonal, then a flat tail into the icon -- on the side opposite
%% the beside-trunk labels, the rotation of the LR off-track idiom.  The trunk
%% descent along the flow axis must not be read as a downward branch (which
%% would flip the output onto the label side).
%%metro line: core | Core | #2db572

%%metro file: trimmed_out | FASTQ
%%metro file: recal_out | CRAM
%%metro off_track: trimmed_out
%%metro off_track: recal_out

graph LR
    subgraph pre [Pre-processing]
        %%metro direction: TB
        fastp[fastp]
        align[align]
        markdup[markduplicates]
        recal[recalibrate]
        collect[collect metrics]
        trimmed_out[ ]
        recal_out[ ]

        fastp -->|core| align
        align -->|core| markdup
        markdup -->|core| recal
        recal -->|core| collect

        fastp -->|core| trimmed_out
        recal -->|core| recal_out
    end

CLI command

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

Rendered map

Tb Offtrack Fork Baseline

A `direction: TB` section with an asymmetric fork whose branch (markduplicates) overshoots the trunk toward the lift side. The off-track downward-branch test anchors its trunk baseline to the through-trunk column rather than the lift-most station, so main-trunk producers downstream of the fork keep their off-track outputs on the lift side instead of flipping them onto the beside-trunk label side (issue #1388).

Mermaid source

%%metro title: TB off-track fork baseline
%% Regression for #1388: in a `direction: TB` section an asymmetric fork sends
%% one branch (markduplicates) further toward the lift side than the trunk.
%% The off-track "downward branch" test derives the trunk baseline on the cross
%% axis; taking the lift-most on-track station let that fork branch become the
%% baseline, so every main-trunk producer downstream (mosdepth, applybqsr) read
%% as a branch and its off-track output flipped onto the beside-trunk label
%% side, colliding with a neighbour label.  The baseline must anchor to the
%% trunk column the through-line runs on, not the lift-most extreme.
%%metro font_scale: 1.34
%%metro line: core | Core | #2db572
%%metro line: alt | Alt | #d62728
%%metro file: samtools_out | CRAM
%%metro file: recal_out | CRAM
%%metro off_track: samtools_out
%%metro off_track: recal_out

graph LR
    subgraph prep [Pre-processing]
        %%metro direction: TB
        a[convert]
        b[FastQC]
        c[mapping]
        d1[bam convert]
        d2[markduplicates]
        h[mosdepth, samtools]
        i[prepare recalibration]
        j[applybqsr]
        k[mosdepth, samtools]
        l[NGSCheckmate]

        a -->|core| b
        b -->|core| c
        c -->|core| d1
        c -->|alt| d2
        d1 -->|core| h
        d2 -->|alt| h
        h -->|core| samtools_out
        h -->|core| i
        i -->|core| j
        j -->|core| recal_out
        j -->|core| k
        k -->|core| l
    end

CLI command

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

Rendered map

Rail Inter Section

Two `%%metro line_spread: rails` sections joined by an inter-section edge. The connector wraps cleanly from the upstream right exit port, down the right margin, across the inter-section gap, and down the left margin into the downstream left entry port - no dangling port stubs and no avoidable crossings between co-travelling lines.

Mermaid source

%%metro title: Rail inter-section connector
%%metro style: dark
%%metro line_spread: rails
%%metro line: a | A | #2db572
%%metro line: b | B | #f4a300

graph LR
    subgraph one [Section one]
        s1[Start]
        s2[Middle]
        s1 -->|a,b| s2
    end
    subgraph two [Section two]
        t1[Next]
        t2[End]
        t1 -->|a,b| t2
    end
    s2 -->|a,b| t1

CLI command

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

Rendered map

Rail Offtrack Io

A `%%metro line_spread: rails` section with off-track `%%metro file:` input and output. Each off-track file terminus carries a buffer-stop nub at the rail-side end of its vertical stub (like the on-rail CRAM/VCF termini) seated clear of its under-icon caption, rather than the line ending bare at the icon.

Mermaid source

%%metro title: Rail off-track file input and output
%%metro style: dark
%%metro line_spread: rails
%%metro line: a | A | #2db572
%%metro line: b | B | #f4a300
%%metro file: cram_in | CRAM
%%metro file: aux_in | BED | Targets
%%metro file: side_out | QC
%%metro off_track: aux_in
%%metro off_track: side_out

graph LR
    subgraph sec [Calling]
        cram_in[ ]
        align[Align]
        call[Call]
        report[Report]
        aux_in[ ]
        side_out[ ]

        cram_in -->|a,b| align
        align -->|a,b| call
        call -->|a,b| report
        aux_in -->|a| call
        call -->|a| side_out
    end

CLI command

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

Rendered map

Rail Offtrack Plain Io

A `%%metro line_spread: rails` section with plain (non-file) off-track input and output. Each plain off-track node renders a station marker at its line end rather than a bare stub, and the input's label sits above the node clear of its drop and the adjacent station's label.

Mermaid source

%%metro title: Rail off-track plain input and output
%%metro style: dark
%%metro line_spread: rails
%%metro line: a | A | #2db572
%%metro line: b | B | #f4a300
%%metro file: cram_in | CRAM

graph LR
    subgraph sec [Calling]
        cram_in[ ]
        align[Align]
        call[Call]
        report[Report]
        aux[Targets BED]
        qc[QC report]

        cram_in -->|a,b| align
        align -->|a,b| call
        call -->|a,b| report
        aux -->|a| call
        call -->|a| qc
    end
%%metro off_track: aux
%%metro off_track: qc

CLI command

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

Rendered map