Packed Cell Cellmate Bypass Adjacent

Gallery / Serpentine Layout

The packed-cell cell-mate bypass with the bypassing line's source section sitting in the column immediately adjacent to the packed cell, with no gap column to descend through. The bypass must still loop below the cell-mate's box rather than collapse back to a straight run through its interior (issue #1233).

Mermaid source

examples/topologies/packed_cell_cellmate_bypass_adjacent.mmd

%%metro title: Packed-cell non-consumer bypass (adjacent source)
%%metro style: nfcore
%%metro fold_threshold: 15
%%metro file: fastq_in | FASTQ
%%metro file: report_out | HTML
%%metro line: dna | DNA (Tumor + Normal) | #4a90d9
%%metro line: rna | RNA (Tumor) | #e63946
%%metro line: realignment | Realignment (RNA) | #f5c542
%%metro line_order: definition
%%metro legend: bl
%%metro grid: preprocessing | 0,0
%%metro grid: gatk_preproc, variant_calling | 1,0
%%metro grid: normalization | 2,0
%%metro grid: consensus | 2,1
%%metro grid: realign, reporting | 1,1

graph LR
    subgraph preprocessing [Pre-processing & Alignment]
        fastq_in[ ]
        fastqc[FastQC]
        fastp[fastp]
        bwa_mem[BWA-mem/BWA-mem2]
        star[STAR]
        samtools_merge[SAMtools Merge]

        fastq_in -->|dna,rna| fastqc
        fastqc -->|dna,rna| fastp
        fastp -->|dna| bwa_mem
        fastp -->|rna| star
        bwa_mem -->|dna| samtools_merge
        star -->|rna| samtools_merge
    end

    subgraph gatk_preproc [GATK Preprocessing]
        markduplicates[MarkDuplicates]
        splitncigar[SplitNCigarReads]
        baserecalibrator[BaseRecalibrator]
        applybqsr[ApplyBQSR]
        samtools_stats[SAMtools Stats]
        mosdepth[Mosdepth]

        markduplicates -->|dna| baserecalibrator
        markduplicates -->|rna| splitncigar
        splitncigar -->|rna| baserecalibrator
        baserecalibrator -->|dna,rna| applybqsr
        applybqsr -->|dna,rna| samtools_stats
        samtools_stats -->|dna,rna| mosdepth
    end

    subgraph variant_calling [Variant Calling (parallel)]
        vc_fork[ ]
        mutect2[Mutect2]
        strelka[Strelka2]
        sage[SAGE]
        vc_join[ ]

        vc_fork -->|dna,rna| mutect2
        vc_fork -->|dna,rna| strelka
        vc_fork -->|dna,rna| sage
        mutect2 -->|dna,rna| vc_join
        strelka -->|dna,rna| vc_join
        sage -->|dna,rna| vc_join
    end

    subgraph normalization [Normalization & Annotation]
        %%metro exit: bottom | dna, rna
        vt_decompose[VT Decompose]
        vt_normalize[VT Normalize]
        ensemblvep[Ensembl VEP]

        vt_decompose -->|dna,rna| vt_normalize
        vt_normalize -->|dna,rna| ensemblvep
    end

    subgraph consensus [Consensus & Filtering]
        %%metro direction: RL
        %%metro entry: top | dna, rna
        %%metro exit: left | rna, realignment
        vcf2maf[vcf2MAF]
        run_consensus[Consensus]
        maf_filtering[MAF Filtering]

        vcf2maf -->|dna,rna| run_consensus
        run_consensus -->|dna,rna| maf_filtering
    end

    subgraph realign [Realignment (RNA)]
        %%metro direction: RL
        %%metro entry: right | realignment
        %%metro exit: left | realignment
        maf2bed[MAF2BED]
        extract_reads[Extract Reads]
        hisat2[HISAT2]
        markdup_re[MarkDuplicates]
        splitncigar_re[SplitNCigarReads]
        bqsr_re[BQSR]
        varcall_re[Variant Calling]
        norm_re[Normalization]
        annotate_re[Annotation]
        consensus_re[Consensus]
        filter_re[MAF Filtering]

        maf2bed -->|realignment| extract_reads
        extract_reads -->|realignment| hisat2
        hisat2 -->|realignment| markdup_re
        markdup_re -->|realignment| splitncigar_re
        splitncigar_re -->|realignment| bqsr_re
        bqsr_re -->|realignment| varcall_re
        varcall_re -->|realignment| norm_re
        norm_re -->|realignment| annotate_re
        annotate_re -->|realignment| consensus_re
        consensus_re -->|realignment| filter_re
    end

    subgraph reporting [Reporting]
        %%metro direction: RL
        %%metro entry: right | rna, realignment
        rna_filter[RNA MAF Filtering]
        rna_filter -->|rna,realignment| multiqc
        multiqc[MultiQC]
        report_out[ ]

        multiqc -->|rna,realignment| report_out
    end

    %% Inter-section edges
    maf_filtering -->|realignment| maf2bed
    samtools_merge -->|dna,rna| markduplicates
    mosdepth -->|dna,rna| vc_fork
    vc_join -->|dna,rna| vt_decompose
    ensemblvep -->|dna,rna| vcf2maf
    filter_re -->|realignment| rna_filter
    maf_filtering -->|rna| rna_filter

CLI command

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

Rendered map