Genomeassembly Staggered

Gallery / Realistic Pipelines

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