Differentialabundance

Gallery / Realistic Pipelines

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