Genomic Pipeline

Gallery / Realistic Pipelines

Multi-section genomic variant-calling pipeline: same-direction sections stacked in one column (serpentine carriage-return) plus a multi-row QC collector fan-in descending a shared inter-column corridor.

Mermaid source

examples/genomic_pipeline.mmd

%%metro title: Variant Calling Pipeline
%%metro style: dark
%%metro legend: br
%%metro line_order: definition
%%metro center_ports: true
%%metro compact_offsets: true
%%metro file: fastq_in | FASTQ
%%metro file: bam_in | BAM
%%metro file: cram_in | CRAM
%%metro file: vcf_out | VCF
%%metro file: report_out | HTML
%%metro line: germline | Germline | #0570b0
%%metro line: tumor_only | Tumor only | #d62728
%%metro line: somatic | Tumor-normal pair | #756bb1

graph LR
    subgraph preprocessing [Pre-processing]
        %%metro exit: right | germline, tumor_only, somatic
        fastq_in[ ]
        bam_in[ ]
        fastqc[FastQC]
        fastp[FastP]
        umi[UMI consensus]
        bwa[BWA-MEM]
        bwa2[BWA-MEM2]
        dragmap[DragMap]
        sentieon_bwa[Sentieon BWA]
        merge_index[samtools merge/index]
        markdup[MarkDuplicates]
        sentieon_dedup[Sentieon Dedup]
        bqsr[BaseRecalibrator]
        applybqsr[ApplyBQSR]
        mosdepth[mosdepth]
        ngscheckmate[NGSCheckmate]

        fastq_in -->|germline,tumor_only,somatic| fastqc
        fastq_in -->|germline,tumor_only,somatic| fastp
        bam_in -->|germline,tumor_only,somatic| fastp
        fastp -->|germline,tumor_only,somatic| umi
        umi -->|germline,tumor_only,somatic| bwa
        umi -->|germline,tumor_only,somatic| bwa2
        umi -->|germline,tumor_only,somatic| dragmap
        umi -->|germline,tumor_only,somatic| sentieon_bwa
        bwa -->|germline,tumor_only,somatic| merge_index
        bwa2 -->|germline,tumor_only,somatic| merge_index
        dragmap -->|germline,tumor_only,somatic| merge_index
        sentieon_bwa -->|germline,tumor_only,somatic| merge_index
        merge_index -->|germline,tumor_only,somatic| markdup
        merge_index -->|germline,tumor_only,somatic| sentieon_dedup
        markdup -->|germline,tumor_only,somatic| bqsr
        sentieon_dedup -->|germline,tumor_only,somatic| bqsr
        bqsr -->|germline,tumor_only,somatic| applybqsr
        applybqsr -->|germline,tumor_only,somatic| mosdepth
        applybqsr -->|germline,tumor_only,somatic| ngscheckmate
    end

    subgraph variant_calling [Variant calling]
        %%metro entry: left | germline, tumor_only, somatic
        %%metro exit: right | germline, tumor_only, somatic
        cram_in[ ]
        haplotypecaller[HaplotypeCaller]
        deepvariant[DeepVariant]
        sentieon_dnascope[Sentieon DNAscope]
        sentieon_haplotyper[Sentieon Haplotyper]
        freebayes[FreeBayes]
        strelka[Strelka]
        mpileup[bcftools mpileup]
        mutect2[Mutect2]
        lofreq[LoFreq]
        muse[MuSE]
        sentieon_tnscope[Sentieon TNscope]
        manta[Manta]
        tiddit[TIDDIT]
        ascat[ASCAT]
        cnvkit[CNVkit]
        controlfreec[Control-FREEC]
        indexcov[indexcov]
        msisensor2[MSIsensor2]
        msisensorpro[MSIsensor-pro]
        vcfs[ ]

        cram_in -->|germline| haplotypecaller
        cram_in -->|germline| deepvariant
        cram_in -->|germline| sentieon_dnascope
        cram_in -->|germline| sentieon_haplotyper
        cram_in -->|germline,tumor_only,somatic| freebayes
        cram_in -->|germline,somatic| strelka
        cram_in -->|germline,tumor_only,somatic| mpileup
        cram_in -->|tumor_only,somatic| mutect2
        cram_in -->|tumor_only| lofreq
        cram_in -->|somatic| muse
        cram_in -->|tumor_only,somatic| sentieon_tnscope
        cram_in -->|germline,tumor_only,somatic| manta
        cram_in -->|germline,tumor_only,somatic| tiddit
        cram_in -->|somatic| ascat
        cram_in -->|germline,tumor_only,somatic| cnvkit
        cram_in -->|tumor_only,somatic| controlfreec
        cram_in -->|germline,somatic| indexcov
        cram_in -->|tumor_only| msisensor2
        cram_in -->|somatic| msisensorpro

        haplotypecaller -->|germline| vcfs
        deepvariant -->|germline| vcfs
        sentieon_dnascope -->|germline| vcfs
        sentieon_haplotyper -->|germline| vcfs
        freebayes -->|germline,tumor_only,somatic| vcfs
        strelka -->|germline,somatic| vcfs
        mpileup -->|germline,tumor_only,somatic| vcfs
        mutect2 -->|tumor_only,somatic| vcfs
        lofreq -->|tumor_only| vcfs
        muse -->|somatic| vcfs
        sentieon_tnscope -->|tumor_only,somatic| vcfs
        manta -->|germline,tumor_only,somatic| vcfs
        tiddit -->|germline,tumor_only,somatic| vcfs
        ascat -->|somatic| vcfs
        cnvkit -->|germline,tumor_only,somatic| vcfs
        controlfreec -->|tumor_only,somatic| vcfs
        indexcov -->|germline,somatic| vcfs
        msisensor2 -->|tumor_only| vcfs
        msisensorpro -->|somatic| vcfs
    end

    subgraph post_vc [Post-processing]
        filter_vcfs[Filter VCFs]
        normalize[Normalize]
        concatenate[Concatenate]
        consensus[Consensus]
        varlociraptor[Varlociraptor]
        bcftools_stats[bcftools stats]
        vcftools[VCFtools]

        filter_vcfs -->|germline,tumor_only,somatic| normalize
        normalize -->|germline,tumor_only,somatic| concatenate
        concatenate -->|germline,tumor_only,somatic| consensus
        consensus -->|germline,tumor_only,somatic| varlociraptor
        varlociraptor -->|germline,tumor_only,somatic| bcftools_stats
        bcftools_stats -->|germline,tumor_only,somatic| vcftools
    end

    subgraph annotation [Annotation]
        snpeff[snpEff]
        vep[VEP]
        bcftools_ann[bcftools annotate]
        snpsift[SnpSift]

        snpeff -->|germline,tumor_only,somatic| vep
        vep -->|germline,tumor_only,somatic| bcftools_ann
        bcftools_ann -->|germline,tumor_only,somatic| snpsift
    end

    subgraph reporting [Reporting]
        multiqc[MultiQC]
        vcf_out[ ]
        report_out[ ]

        multiqc -->|germline,tumor_only,somatic| report_out
        snpsift_to_vcf[ ]
        snpsift_to_vcf -->|germline,tumor_only,somatic| vcf_out
    end

    %% Inter-section edges
    applybqsr -->|germline,tumor_only,somatic| cram_in
    vcfs -->|germline,tumor_only,somatic| filter_vcfs
    vcftools -->|germline,tumor_only,somatic| snpeff
    snpsift -->|germline,tumor_only,somatic| snpsift_to_vcf
    fastqc -->|germline,tumor_only,somatic| multiqc
    mosdepth -->|germline,tumor_only,somatic| multiqc
    bcftools_stats -->|germline,tumor_only,somatic| multiqc

CLI command

nf-metro render examples/genomic_pipeline.mmd -o genomic_pipeline.svg

Rendered map