Rowmate Tb Side Entry Top Align

Gallery / Realistic Pipelines

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

examples/topologies/rowmate_tb_side_entry_top_align.mmd

%%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