Off Track Input Above Consumer

Gallery / Off-track & Rails

A section whose mid-trunk station consumes an off-track input while a neighbouring station feeds an off-track output. The input hugs one row above its consumer instead of towering an extra slot up because it shares an anchor with the differently-columned output (issue #651).

Mermaid source

%%metro title: Long-read Methylation & Variant Atlas
%%metro style: dark
%%metro line: dna | DNA variants | #2db572
%%metro line: rna | RNA expression | #e63946
%%metro line: qc | QC stream | #f4a261

%%metro file: ref_fa | FASTA | Reference
%%metro file: gtf_in | GTF | Annotation
%%metro file: cpg_bed | BED | CpG islands
%%metro off_track: ref_fa, gtf_in, cpg_bed

%%metro file: raw_bam | BAM | Aligned
%%metro file: meth_bw | bigWig | Methylation
%%metro off_track: raw_bam, meth_bw

graph LR
    subgraph intake [Intake & Basecall]
        in_pod5[POD5]
        in_basecall[Basecall]
        in_demux[Demux]
        in_qc[ReadQC]

        in_pod5 -->|dna,rna,qc| in_basecall
        in_basecall -->|dna,rna,qc| in_demux
        in_demux -->|dna,rna,qc| in_qc
    end

    subgraph align [Alignment]
        ref_fa[ ]
        gtf_in[ ]
        al_minimap[minimap2]
        al_sort[Sort]
        al_index[Index]
        raw_bam[ ]

        ref_fa -->|dna,rna| al_minimap
        gtf_in -->|rna| al_minimap
        al_minimap -->|dna,rna,qc| al_sort
        al_sort -->|dna,rna,qc| al_index
        al_sort -->|dna| raw_bam
    end

    subgraph methcall [Methylation Calling]
        mc_modkit[modkit]
        mc_pileup[Pileup]
        mc_dmr[DMR]
        cpg_bed[ ]
        meth_bw[ ]

        cpg_bed -->|dna| mc_pileup
        mc_modkit -->|dna| mc_pileup
        mc_pileup -->|dna| mc_dmr
        mc_pileup -->|dna| meth_bw
    end

    subgraph variants [Variant Calling]
        vc_clair[Clair3]
        vc_phase[Phase]
        vc_filter[Filter]

        vc_clair -->|dna| vc_phase
        vc_phase -->|dna| vc_filter
    end

    subgraph expr [Expression]
        ex_isoquant[IsoQuant]
        ex_count[Count]
        ex_norm[Normalize]

        ex_isoquant -->|rna| ex_count
        ex_count -->|rna| ex_norm
    end

    subgraph fusion [Fusion Detection]
        fu_jaffal[JAFFAL]
        fu_annotate[Annotate]

        fu_jaffal -->|rna| fu_annotate
    end

    subgraph merge [Merge & Annotate]
        mg_collect[Collect]
        mg_vep[VEP]
        mg_classify[Classify]

        mg_collect -->|dna,rna| mg_vep
        mg_vep -->|dna,rna| mg_classify
    end

    subgraph report [Report]
        rp_aggregate[Aggregate]
        rp_multiqc[MultiQC]
        rp_final[Report]

        rp_aggregate -->|dna,rna,qc| rp_multiqc
        rp_multiqc -->|dna,rna,qc| rp_final
    end

    in_qc -->|dna,rna,qc| al_minimap
    al_index -->|dna| mc_modkit
    al_index -->|dna| vc_clair
    al_index -->|rna| ex_isoquant
    al_index -->|rna| fu_jaffal
    al_index -->|qc| rp_aggregate
    mc_dmr -->|dna| mg_collect
    vc_filter -->|dna| mg_collect
    ex_norm -->|rna| mg_collect
    fu_annotate -->|rna| mg_collect
    mg_classify -->|dna,rna| rp_aggregate

CLI command

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

Rendered map