Gallery

Rendered examples covering a range of layout patterns. Click any heading in the right-hand table of contents to jump to an example.

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Main Examples

Simple Pipeline

Minimal two-line pipeline with no sections.

CLI command:

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

Mermaid source

%%metro title: Simple Pipeline
%%metro style: dark
%%metro line: main | Main | #4CAF50
%%metro line: qc | Quality Control | #2196F3 | dashed

graph LR
    input[Input]
    fastqc[FastQC]
    trim[Trimming]
    align[Alignment]
    quant[Quantification]
    multiqc[MultiQC]

    input -->|main| trim
    trim -->|main| align
    align -->|main| quant
    input -->|qc| fastqc
    trim -->|qc| fastqc
    quant -->|qc| multiqc
    fastqc -->|qc| multiqc

Rendered output:

Rnaseq Auto

Demonstrates fully auto-inferred layout: no %%metro grid: directives needed. See nf-core Pipelines for the full gallery.

CLI command:

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

Mermaid source

%%metro title: nf-core/rnaseq
%%metro logo: examples/nf-core-rnaseq_logo_dark.png
%%metro style: dark
%%metro line: star_rsem | Aligner: STAR, Quantification: RSEM | #0570b0
%%metro line: star_salmon | Aligner: STAR, Quantification: Salmon (default) | #2db572
%%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

graph LR
    subgraph preprocessing [Pre-processing]
        cat_fastq[cat fastq]
        fastqc_raw[FastQC]
        infer_strandedness[infer strandedness]
        umi_tools_extract[UMI-tools extract]
        fastp[FastP]
        trimgalore[Trim Galore!]
        fastqc_trimmed[FastQC]
        bbsplit[BBSplit]
        sortmerna[SortMeRNA]

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

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

        fastqc_trimmed -->|star_salmon,star_rsem,hisat2,pseudo_salmon,pseudo_kallisto| bbsplit
        bbsplit -->|star_salmon,star_rsem,hisat2,pseudo_salmon,pseudo_kallisto| sortmerna
    end

    subgraph genome_align [Genome alignment & quantification]
        star[STAR]
        hisat2_align[HISAT2]
        rsem[RSEM]
        salmon_quant[Salmon]
        umi_tools_dedup[UMI-tools dedup]

        star -->|star_rsem| rsem
        star -->|star_salmon| umi_tools_dedup
        umi_tools_dedup -->|star_salmon| salmon_quant
        hisat2_align -->|hisat2| umi_tools_dedup
    end

    subgraph postprocessing [Post-processing]
        samtools[SAMtools]
        picard[Picard]
        bedtools[BEDTools]
        bedgraph[bedGraphToBigWig]
        stringtie[StringTie]

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

    subgraph pseudo_align [Pseudo-alignment & quantification]
        salmon_pseudo[Salmon]
        kallisto[Kallisto]
        multiqc_pseudo[MultiQC]

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

    subgraph qc_report [Quality control & reporting]
        rseqc[RSeQC]
        preseq[Preseq]
        qualimap[Qualimap]
        dupradar[dupRadar]
        deseq2_pca[DESeq2 PCA]
        kraken2[Kraken2/Bracken]
        multiqc_final[MultiQC]

        rseqc -->|star_salmon,star_rsem,hisat2| preseq
        preseq -->|star_salmon,star_rsem,hisat2| qualimap
        qualimap -->|star_salmon,star_rsem,hisat2| dupradar
        dupradar -->|star_salmon,star_rsem,hisat2| deseq2_pca
        deseq2_pca -->|star_salmon,star_rsem,hisat2| kraken2
        kraken2 -->|star_salmon,star_rsem,hisat2| multiqc_final
    end

    %% Inter-section edges
    sortmerna -->|star_salmon,star_rsem| star
    sortmerna -->|hisat2| hisat2_align
    sortmerna -->|pseudo_salmon| salmon_pseudo
    sortmerna -->|pseudo_kallisto| kallisto
    salmon_quant -->|star_salmon| samtools
    rsem -->|star_rsem| samtools
    umi_tools_dedup -->|hisat2| samtools
    stringtie -->|star_salmon,star_rsem,hisat2| rseqc

Rendered output:

Rnaseq Sections

Same pipeline with manual %%metro grid: overrides and file markers, showing how explicit directives can fine-tune placement.

CLI command:

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

Mermaid source

%%metro title: nf-core/rnaseq
%%metro logo: examples/nf-core-rnaseq_logo_dark.png
%%metro style: dark
%%metro file: fastq_in | FASTQ
%%metro file: report_final | HTML
%%metro file: report_quant | HTML
%%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: hisat2 | Aligner: HISAT2, Quantification: None | #f5c542
%%metro line: bowtie2_salmon | Aligner: Bowtie2, Quantification: Salmon | #ff8c00
%%metro line: pseudo_salmon | Pseudo-aligner: Salmon, Quantification: Salmon | #e63946
%%metro line: pseudo_kallisto | Pseudo-aligner: Kallisto, Quantification: Kallisto | #7b2d3b
%%metro legend: bl

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]
        infer_strandedness[Infer Strandedness]
        umi_tools_extract[UMI-tools Extract]
        fastp[fastp]
        trimgalore[Trim Galore!]
        fastqc_trimmed[FastQC]
        bbsplit[BBSplit]
        sortmerna[SortMeRNA]
        ribodetector[RiboDetector]
        fastqc_filtered[FastQC]

        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| infer_strandedness
        infer_strandedness -->|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
        fastqc_trimmed -->|pseudo_salmon,pseudo_kallisto,star_salmon,star_rsem,hisat2,bowtie2_salmon| sortmerna
        fastqc_trimmed -->|pseudo_salmon,pseudo_kallisto,star_salmon,star_rsem,hisat2,bowtie2_salmon| ribodetector
        bbsplit -->|pseudo_salmon,pseudo_kallisto,star_salmon,star_rsem,hisat2,bowtie2_salmon| fastqc_filtered
        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
    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| rsem
        star -->|star_salmon| umi_tools_dedup
        hisat2_align -->|hisat2| umi_tools_dedup
        bowtie2_align -->|bowtie2_salmon| umi_tools_dedup
        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 pseudo_align [Pseudo-alignment & quantification]
        %%metro entry: left | pseudo_salmon, pseudo_kallisto
        salmon_pseudo[Salmon]
        kallisto[Kallisto]
        tximport_pa[tximport]
        summarized_exp_pa[Sum. Exp.]
        multiqc_quant[MultiQC]
        report_quant[ ]

        salmon_pseudo -->|pseudo_salmon| tximport_pa
        kallisto -->|pseudo_kallisto| tximport_pa
        tximport_pa -->|pseudo_salmon,pseudo_kallisto| summarized_exp_pa
        summarized_exp_pa -->|pseudo_salmon,pseudo_kallisto| multiqc_quant
        multiqc_quant -->|pseudo_salmon,pseudo_kallisto| report_quant
    end

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

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

    subgraph qc_report [Quality control & reporting]
        %%metro direction: RL
        %%metro entry: top | star_salmon, star_rsem, hisat2
        rseqc[RSeQC]
        preseq[Preseq]
        qualimap[Qualimap]
        dupradar[dupRadar]
        featurecounts[featureCounts]
        deseq2_pca[DESeq2 PCA]
        kraken2[Kraken2/Bracken]
        sylph[Sylph]
        multiqc_final[MultiQC]
        report_final[ ]

        rseqc -->|star_salmon,star_rsem,hisat2| preseq
        preseq -->|star_salmon,star_rsem,hisat2| qualimap
        qualimap -->|star_salmon,star_rsem,hisat2| dupradar
        dupradar -->|star_salmon,star_rsem,hisat2| featurecounts
        featurecounts -->|star_salmon,star_rsem,hisat2| deseq2_pca
        deseq2_pca -->|star_salmon,star_rsem,hisat2| kraken2
        deseq2_pca -->|star_salmon,star_rsem,hisat2| sylph
        kraken2 -->|star_salmon,star_rsem,hisat2| multiqc_final
        sylph -->|star_salmon,star_rsem,hisat2| multiqc_final
        multiqc_final -->|star_salmon,star_rsem,hisat2| report_final
    end

    %% Inter-section edges
    fastqc_filtered -->|star_salmon,star_rsem| star
    fastqc_filtered -->|hisat2| hisat2_align
    fastqc_filtered -->|bowtie2_salmon| bowtie2_align
    fastqc_filtered -->|pseudo_salmon| salmon_pseudo
    fastqc_filtered -->|pseudo_kallisto| kallisto
    summarized_exp_ga -->|star_salmon,star_rsem| samtools
    _h3 -->|hisat2| samtools
    stringtie -->|star_salmon,star_rsem,hisat2| rseqc

Rendered output:

Differentialabundance

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

CLI command:

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

Mermaid source

%%metro title: nf-core/differentialabundance
%%metro logo: nf-core-differentialabundance_logo_dark.png
%%metro style: dark
%%metro legend: br
%%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

Rendered output:

Differentialabundance Default

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

CLI command:

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

Mermaid source

%%metro title: nf-core/differentialabundance
%%metro logo: nf-core-differentialabundance_logo_dark.png
%%metro style: dark
%%metro legend: br
%%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

Rendered output:

Genomeassembly Staggered

sanger-tol/genomeassembly with explicit %%metro grid: directives stacking each section in its own grid row. Regression fixture for #250 (cross-column junction routes were going backward in X).

CLI command:

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

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

Rendered output:

---

Simple Topologies

Single Section

One section, one line. The simplest possible case.

CLI command:

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

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

Rendered output:

Deep Linear

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

CLI command:

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

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

Rendered output:

Parallel Independent

Two disconnected pipelines stacked vertically.

CLI command:

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

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

Rendered output:

---

Fan-out and Fan-in

Wide Fan Out

One source fanning out to four target sections.

CLI command:

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

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

Rendered output:

Wide Fan In

Four sources converging into one target section.

CLI command:

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

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

Rendered output:

Section Diamond

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

CLI command:

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

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

Rendered output:

---

Branching and Multipath

Asymmetric Tree

One root branching into three paths of different depths.

CLI command:

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

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

Rendered output:

Complex Multipath

Four lines taking different routes through six sections.

CLI command:

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

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

Rendered output:

---

Multi-line Bundles

Multi Line Bundle

Six lines travelling through the same three-section chain.

CLI command:

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

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

Rendered output:

Mixed Port Sides

A section with both RIGHT and BOTTOM exits.

CLI command:

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

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

Rendered output:

---

Realistic Pipelines

Rnaseq Lite

Simplified RNA-seq pipeline with three analysis routes.

CLI command:

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

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

Rendered output:

Variant Calling

Variant calling pipeline with four lines sharing alignment.

CLI command:

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

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

Rendered output:

---

Fold Topologies

Fold Fan Across

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

CLI command:

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

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

Rendered output:

Fold Double

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

CLI command:

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

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

Rendered output:

Fold Stacked Branch

Stacked analysis sections feeding through a fold into branching targets.

CLI command:

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

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

Rendered output:

Mismatched Tracks

Lines with mismatched track counts at shared stations.

CLI command:

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

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

Rendered output:

Upward Bypass

Tall section bypass where the trunk is above the source (upward gap1).

CLI command:

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

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

Rendered output:

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.

CLI command:

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

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

Rendered output: