Row Trunk Partial Through Line

Gallery / Inter-section Routing

Three sections share one grid cell along a row. The last of them is entered by a single line of the row's three-line bundle, and the junction feeding it fans that same line into a section in the row below. The section still carries part of the row's trunk, so its interior sits on the row's trunk Y and its hybrid-GTF output peels one lane above, rather than the whole trunk being recentred in the shorter box (issue #1844).

Mermaid source

examples/topologies/row_trunk_partial_through_line.mmd

%%metro title: Row Trunk Partial Through Line
%%metro style: dark
%%metro file: bigwig_out | BW | Coverage
%%metro file: counts_out | TSV | Gene counts
%%metro file: gtf_out | GTF | Hybrid GTF
%%metro file: te_out | TSV | TE results
%%metro file: preqc_out | HTML | Pre-QC
%%metro line: riboseq | Ribo-seq | #e6007e
%%metro line: rnaseq | RNA-seq | #2db572
%%metro line: tiseq | TI-seq | #2b6cb0

%%metro grid: preprocessing, alignment, novel_transcripts | 0,0
%%metro grid: te | 0,1

graph LR
    subgraph preprocessing [Read pre-processing]
        fastp[fastp]
        bbsplit[BBSplit]
        sortmerna[SortMeRNA]
        ribodetector[RiboDetector]
        equalise[Equalise]

        fastp -->|riboseq,rnaseq,tiseq| bbsplit
        bbsplit -->|riboseq,rnaseq,tiseq| preqc_out
        bbsplit -->|riboseq,rnaseq,tiseq| sortmerna
        bbsplit -->|riboseq,rnaseq,tiseq| ribodetector
        sortmerna -->|riboseq,rnaseq,tiseq| equalise
        ribodetector -->|riboseq,rnaseq,tiseq| equalise
    end

    subgraph alignment [Alignment & quantification]
        star[STAR]
        umi_dedup[UMI dedup]
        genomecov[genomecov]
        salmon[Salmon]

        star -->|riboseq,rnaseq,tiseq| umi_dedup
        umi_dedup -->|riboseq,rnaseq,tiseq| genomecov
        umi_dedup -->|riboseq,rnaseq,tiseq| salmon
        genomecov -->|riboseq,rnaseq,tiseq| bigwig_out
        salmon -->|riboseq,rnaseq,tiseq| counts_out
    end

    subgraph novel_transcripts [Transcript discovery]
        stringtie[StringTie]
        gffcompare[gffcompare]
        merge_gtf[Merge GTF]

        stringtie -->|rnaseq| gffcompare
        gffcompare -->|rnaseq| merge_gtf
        merge_gtf -->|rnaseq| gtf_out
    end

    subgraph te [Translational efficiency]
        counts[Count matrix]
        deltate[deltaTE]

        counts -->|rnaseq| deltate
        deltate -->|rnaseq| te_out
    end

    equalise -->|riboseq,rnaseq,tiseq| star
    umi_dedup -->|rnaseq| stringtie
    umi_dedup -->|rnaseq| counts
    merge_gtf -->|rnaseq| counts

CLI command

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

Rendered map