Aligner Row Terminator Lane Gap

Gallery / Multi-line Bundles

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