nf-core pipelines

Real-world pipelines rendered with nf-metro. See the Gallery for layout pattern examples and the Guide for how to write your own.

nf-core/epitopeprediction

MHC binding prediction from VCF, protein FASTA, or peptide TSV inputs through five prediction tools. GitHub

Mermaid source

%%metro title: nf-core/epitopeprediction
%%metro style: dark
%%metro line_order: span
%%metro logo: examples/nf-core-epitopeprediction_logo_light.png | examples/nf-core-epitopeprediction_logo_dark.png
%%metro legend: bl
%%metro line: vcf | Variant Input | #2db572
%%metro line: protein | Protein Input | #e6550d
%%metro line: peptide | Peptide Input | #756bb1
%%metro file: VCF_IN | VCF
%%metro file: FASTA_IN | FASTA
%%metro file: TSV_IN | TSV
%%metro file: TSV_OUT | TSV
%%metro file: HTML_OUT | HTML

graph LR
    subgraph input_processing [Input Processing]
        VCF_IN[ ]
        gunzip_vcf([Gunzip VCF])
        snpsift_split([SnpSift Split])
        variant_pred([Variant Pred])
        FASTA_IN[ ]
        fasta2peptides([Fasta2Peptides])
        TSV_IN[ ]

        VCF_IN -->|vcf| gunzip_vcf
        gunzip_vcf -->|vcf| snpsift_split
        snpsift_split -->|vcf| variant_pred
        FASTA_IN -->|protein| fasta2peptides
    end

    subgraph binding_prediction [Binding Prediction]
        split_peptides([Split Peptides])
        prepare_input([Prepare Input])
        mhcflurry([MHCflurry])
        mhcnuggets([MHCnuggets])
        mhcnuggetsii([MHCnuggetsII])
        netmhcpan([NetMHCpan])
        netmhciipan([NetMHCIIpan])
        merge_pred([Merge Pred])

        split_peptides -->|vcf,protein,peptide| prepare_input
        prepare_input -->|vcf,protein,peptide| mhcflurry
        prepare_input -->|vcf,protein,peptide| mhcnuggets
        prepare_input -->|vcf,protein,peptide| mhcnuggetsii
        prepare_input -->|vcf,protein,peptide| netmhcpan
        prepare_input -->|vcf,protein,peptide| netmhciipan
        mhcflurry -->|vcf,protein,peptide| merge_pred
        mhcnuggets -->|vcf,protein,peptide| merge_pred
        mhcnuggetsii -->|vcf,protein,peptide| merge_pred
        netmhcpan -->|vcf,protein,peptide| merge_pred
        netmhciipan -->|vcf,protein,peptide| merge_pred
    end

    subgraph reporting [Reporting]
        summarize([Summarize Results])
        _tsv_pad[ ]
        multiqc([MultiQC])
        TSV_OUT[ ]
        HTML_OUT[ ]

        summarize -->|vcf,protein,peptide| _tsv_pad
        summarize -->|vcf,protein,peptide| multiqc
        _tsv_pad -->|vcf,protein,peptide| TSV_OUT
        multiqc -->|vcf,protein,peptide| HTML_OUT
    end

    %% Inter-section edges
    variant_pred -->|vcf| split_peptides
    fasta2peptides -->|protein| split_peptides
    TSV_IN -->|peptide| split_peptides
    merge_pred -->|vcf,protein,peptide| summarize

CLI command

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

Rendered map

sanger-tol/genomeassembly

Genome assembly from long reads and Hi-C data through purging, polishing, scaffolding, and QC. GitHub

Mermaid source

%%metro title: sanger-tol/genomeassembly
%%metro style: dark
%%metro line: long_reads | Long reads | #2db572
%%metro line: hic_reads | Hi-C reads | #e6842a
%%metro line: i10x_reads | 10X reads | #756bb1
%%metro line: assemblies | Assembly | #0570b0
%%metro file: input_long_reads | FASTX
%%metro file: input_hic_reads | CRAM
%%metro file: input_10x_reads | FASTQ
%%metro line_order: span
%%metro compact_offsets: true
%%metro legend: bl
graph LR
    subgraph raw_asm [Raw assembly]
        %%metro exit: bottom | hic_reads
        %%metro exit: right | assemblies,long_reads
        input_long_reads[ ]
        input_hic_reads[ ]
        hifiasm[Hifiasm]
        input_long_reads -->|long_reads| hifiasm
        input_hic_reads -->|hic_reads| hifiasm
    end
    subgraph purging [Purging]
        %%metro entry: left | assemblies,long_reads
        %%metro exit: right | assemblies
        purging_minimap2[minimap2]
        purge_dups[purge_dups]
        purging_minimap2 -->|assemblies,long_reads| purge_dups
    end
    subgraph polishing [Polishing]
        %%metro entry: left | assemblies
        %%metro exit: right | assemblies
        input_10x_reads[ ]
        longranger[Longranger]
        freebayes[FreeBayes]
        input_10x_reads -->|i10x_reads| longranger
        longranger -->|i10x_reads,assemblies| freebayes
    end
    subgraph scaffolding [Scaffolding]
        %%metro entry: left | assemblies
        %%metro entry: bottom | hic_reads
        %%metro exit: right | assemblies
        scaffolding_bwamem2[bwa-mem2]
        scaffolding_minimap2[minimap2]
        yahs[YaHS]
        pretextmap[PretextMap]
        juicer[Juicer]
        cooler[Cooler]
        scaffolding_bwamem2 -->|assemblies,hic_reads| yahs
        scaffolding_minimap2 -->|assemblies,hic_reads| yahs
        yahs -->|assemblies,hic_reads| pretextmap
        yahs -->|assemblies,hic_reads| juicer
        yahs -->|assemblies,hic_reads| cooler
    end
    subgraph genome_statistics [Genome QC]
        %%metro entry: left | assemblies
        asmstats[asmstats]
        gfastats[GFAStats]
        busco[BUSCO]
        merquryfk[MerquryFK]
        asmstats -->|assemblies| gfastats
        asmstats -->|assemblies| busco
        asmstats -->|assemblies| merquryfk
    end

    %% Inter-section edges
    hifiasm -->|assemblies,long_reads| purging_minimap2
    hifiasm -->|hic_reads| scaffolding_bwamem2
    hifiasm -->|hic_reads| scaffolding_minimap2
    hifiasm -->|assemblies| longranger
    hifiasm -->|assemblies| scaffolding_bwamem2
    hifiasm -->|assemblies| scaffolding_minimap2
    purge_dups -->|assemblies| longranger
    purge_dups -->|assemblies| scaffolding_bwamem2
    purge_dups -->|assemblies| scaffolding_minimap2
    freebayes -->|assemblies| scaffolding_bwamem2
    freebayes -->|assemblies| scaffolding_minimap2
    hifiasm -->|assemblies| asmstats
    purge_dups -->|assemblies| asmstats
    freebayes -->|assemblies| asmstats
    yahs -->|assemblies| asmstats

CLI command

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

Rendered map

nf-core/hlatyping

HLA typing from FASTQ or BAM inputs via OptiType and HLA-HD. GitHub

Mermaid source

%%metro title: nf-core/hlatyping
%%metro style: dark
%%metro logo: examples/nf-core-hlatyping_logo_light.png | examples/nf-core-hlatyping_logo_dark.png
%%metro file: fastq_in | FASTQ
%%metro file: bam_in | BAM
%%metro file: report_tsv | TSV
%%metro file: report_html | HTML
%%metro line: fastq | FASTQ | #2db572
%%metro line: bam | BAM | #e6842a
%%metro legend: bl

graph LR
    subgraph preprocessing [Pre-processing]
        %%metro exit: right | fastq, bam
        fastq_in[ ]
        bam_in[ ]
        cat_fastq[cat FASTQ]
        _fastq_delay[ ]
        check_paired[Check Paired]
        collatefastq[BAM to FASTQ]
        fastqc[FastQC]

        fastq_in -->|fastq| cat_fastq
        cat_fastq -->|fastq| _fastq_delay
        _fastq_delay -->|fastq| fastqc
        bam_in -->|bam| check_paired
        check_paired -->|bam| collatefastq
        collatefastq -->|bam| fastqc
    end

    subgraph hla_typing [HLA Typing]
        %%metro entry: left | fastq, bam
        %%metro exit: right | fastq, bam
        yara_index[Yara Index]
        yara_mapper[Yara Mapper]
        optitype_run[OptiType]
        _hlahd_delay[ ]
        hlahd_run[HLA-HD]
        _hlahd_delay2[ ]
        _merge1[ ]

        yara_index -->|fastq,bam| yara_mapper
        yara_mapper -->|fastq,bam| optitype_run
        optitype_run -->|fastq,bam| _merge1
        _hlahd_delay -->|fastq,bam| hlahd_run
        hlahd_run -->|fastq,bam| _hlahd_delay2
        _hlahd_delay2 -->|fastq,bam| _merge1
    end

    subgraph reporting [Reporting]
        %%metro entry: left | fastq, bam
        report_tsv[ ]
        multiqc[MultiQC]
        report_html[ ]

        multiqc -->|fastq,bam| report_html
    end

    %% Inter-section edges
    fastqc -->|fastq,bam| yara_index
    fastqc -->|fastq,bam| _hlahd_delay
    _merge1 -->|fastq,bam| report_tsv
    _merge1 -->|fastq,bam| multiqc

CLI command

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

Rendered map

nf-core/rnaseq

RNA-seq analysis with multiple aligner and quantification routes (STAR/RSEM, STAR/Salmon, HISAT2, Salmon pseudo-alignment, Kallisto). GitHub

Mermaid source

%%metro title: nf-core/rnaseq
%%metro logo: examples/nf-core-rnaseq_logo_light.png | examples/nf-core-rnaseq_logo_dark.png
%%metro style: dark
%%metro line: star_rsem | Aligner: STAR, Quantification: RSEM | #0570b0
%%metro line: star_salmon | Aligner: STAR, Quantification: Salmon (default) | #2db572
%%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: 0.6

graph LR
    subgraph preprocessing [Pre-processing]
        cat_fastq[cat fastq]
        fastqc_raw[FastQC]
        infer_strandedness[infer strandedness]
        umi_tools_extract[UMI-tools extract]
        fastp[FastP]
        trimgalore[Trim Galore!]
        fastqc_trimmed[FastQC]
        bbsplit[BBSplit]
        sortmerna[SortMeRNA]

        cat_fastq -->|star_salmon,star_rsem,hisat2,pseudo_salmon,pseudo_kallisto| fastqc_raw
        fastqc_raw -->|star_salmon,star_rsem,hisat2,pseudo_salmon,pseudo_kallisto| infer_strandedness
        infer_strandedness -->|star_salmon,star_rsem,hisat2,pseudo_salmon,pseudo_kallisto| umi_tools_extract

        umi_tools_extract -->|star_salmon,star_rsem,hisat2,pseudo_salmon,pseudo_kallisto| fastp
        umi_tools_extract -->|star_salmon,star_rsem,hisat2,pseudo_salmon,pseudo_kallisto| trimgalore
        fastp -->|star_salmon,star_rsem,hisat2,pseudo_salmon,pseudo_kallisto| fastqc_trimmed
        trimgalore -->|star_salmon,star_rsem,hisat2,pseudo_salmon,pseudo_kallisto| fastqc_trimmed

        fastqc_trimmed -->|star_salmon,star_rsem,hisat2,pseudo_salmon,pseudo_kallisto| bbsplit
        bbsplit -->|star_salmon,star_rsem,hisat2,pseudo_salmon,pseudo_kallisto| sortmerna
    end

    subgraph genome_align [Genome alignment & quantification]
        star[STAR]
        hisat2_align[HISAT2]
        rsem[RSEM]
        salmon_quant[Salmon]
        umi_tools_dedup[UMI-tools dedup]

        star -->|star_rsem| rsem
        star -->|star_salmon| umi_tools_dedup
        umi_tools_dedup -->|star_salmon| salmon_quant
        hisat2_align -->|hisat2| umi_tools_dedup
    end

    subgraph postprocessing [Post-processing]
        samtools[SAMtools]
        picard[Picard]
        bedtools[BEDTools]
        bedgraph[bedGraphToBigWig]
        stringtie[StringTie]

        samtools -->|star_salmon,star_rsem,hisat2| picard
        picard -->|star_salmon,star_rsem,hisat2| bedtools
        bedtools -->|star_salmon,star_rsem,hisat2| bedgraph
        bedgraph -->|star_salmon,star_rsem,hisat2| stringtie
    end

    subgraph pseudo_align [Pseudo-alignment & quantification]
        salmon_pseudo[Salmon]
        kallisto[Kallisto]
        multiqc_pseudo[MultiQC]

        salmon_pseudo -->|pseudo_salmon| multiqc_pseudo
        kallisto -->|pseudo_kallisto| multiqc_pseudo
    end

    subgraph qc_report [Quality control & reporting]
        rseqc[RSeQC]
        preseq[Preseq]
        qualimap[Qualimap]
        dupradar[dupRadar]
        deseq2_pca[DESeq2 PCA]
        kraken2[Kraken2/Bracken]
        multiqc_final[MultiQC]

        rseqc -->|star_salmon,star_rsem,hisat2| preseq
        preseq -->|star_salmon,star_rsem,hisat2| qualimap
        qualimap -->|star_salmon,star_rsem,hisat2| dupradar
        dupradar -->|star_salmon,star_rsem,hisat2| deseq2_pca
        deseq2_pca -->|star_salmon,star_rsem,hisat2| kraken2
        kraken2 -->|star_salmon,star_rsem,hisat2| multiqc_final
    end

    %% Inter-section edges
    sortmerna -->|star_salmon,star_rsem| star
    sortmerna -->|hisat2| hisat2_align
    sortmerna -->|pseudo_salmon| salmon_pseudo
    sortmerna -->|pseudo_kallisto| kallisto
    salmon_quant -->|star_salmon| samtools
    rsem -->|star_rsem| samtools
    umi_tools_dedup -->|hisat2| samtools
    stringtie -->|star_salmon,star_rsem,hisat2| rseqc

CLI command

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

Rendered map

nf-core/sarek

Germline and somatic variant calling, covering germline, tumor-only, and tumor-normal paired analysis through SNP/indel, SV/CNV, and MSI callers with downstream variant annotation. GitHub

Mermaid source

%%metro title: Example analysis pathways
%%metro caption: Adapted from: Fellows Yates, James A., et al. PeerJ 9 (2021)
%%metro style: dark
%%metro logo: examples/nf-core-sarek_logo_light.png | examples/nf-core-sarek_logo_dark.png
%%metro logo_scale: 1.0
%%metro font_scale: 1.3
%%metro legend_logo_gap: 40
%%metro legend: br
%%metro label_angle: 45
%%metro line_spread: rails | calling
%%metro grid: preprocessing | 0,0
%%metro grid: variantcalling | 1,0
%%metro grid: annotation | 2,0
%%metro grid: calling | 0,1,1,3

%%metro line: core | Core workflow | #2db572
%%metro line: germline | Germline | #0570b0
%%metro line: tumor_only | Tumor only | #d62728
%%metro line: pair_n | Tumor-normal (normal) | #0570b0
%%metro line: pair_t | Tumor-normal (tumor) | #d62728

%% Tumor-normal pair is the normal + tumor lines bundled together; give the
%% combination a single legend entry instead of two separate rows.
%%metro legend_combo: pair_n, pair_t | Tumor-normal pair

%%metro files: ubam_in | uBAM
%%metro files: spring_in | spring
%%metro files: fastq_in | FASTQ
%%metro file: vcf_ann | VCF
%%metro file: vcf_vc | VCF
%%metro files: cram_call | CRAM
%%metro file: out | VCF
%%metro file: out | TXT
%%metro files: out | ...

%% Intermediate alignment artefacts written off the trunk at the step that
%% produces them (mapping, samtools, recalibration prep, applybqsr).
%%metro files: mapped_out | BAM/CRAM
%%metro files: samtools_out | CRAM
%%metro files: recalprep_out | CRAM
%%metro files: recal_out | CRAM

%% ubam and spring need conversion, so they feed convert; fastq is already in
%% the right format and joins the trunk at FastQC, past convert.  spring and
%% fastq lift off the trunk as off-track inputs with an S-curve.  The bam/cram
%% outputs hang off their producer the same way (off_track anchors a sink to
%% its source).
%%metro off_track: fastq_in
%%metro off_track: spring_in
%%metro off_track: mapped_out
%%metro off_track: samtools_out
%%metro off_track: recalprep_out
%%metro off_track: recal_out
%%metro off_track: vcf_vc

%% Marker key. Optional steps use the standard station pill (undistinguished);
%% only mandatory / accelerated steps get a marker shape. Acceleration is shown
%% by fill colour: Parabricks (green), Sentieon (navy), or both (teal) on
%% whatever shape the step already carries.
%%metro marker_legend: square, solid | Mandatory
%%metro marker_legend: square, #4CAF50 | Parabricks accelerated
%%metro marker_legend: square, #1b3a6b | Sentieon accelerated
%%metro marker_legend: square, #2f7f74 | Parabricks & Sentieon accelerated
%%metro marker_legend: pill, open | Expanded in pathways panel

%% Caller families along the pathways trunk.
%%metro group: SNPs & Indels | deepvariant, freebayes, haplotypecaller, haplotyper, dnascope, tnscope, lofreq, muse, mpileup, mutect2, strelka2
%%metro group: SV & CNV | indexcov, manta, tiddit, ascat, controlfreec, cnvkit
%%metro group: MSI | msisensor2, msisensorpro

%% --- markers: mandatory steps get a square; acceleration is the fill colour.
%% mapping and markduplicates are accelerable by both Parabricks and Sentieon
%% (teal); the BQSR steps are Parabricks-only (green); the Sentieon callers in
%% the pathways panel are Sentieon-only (navy).
%%metro marker: convert | square, solid
%%metro marker: bam_convert | square, solid
%%metro marker: mapping | square, #2f7f74
%%metro marker: markduplicates | square, #2f7f74
%%metro marker: prepare_recal | circle, #4CAF50
%%metro marker: applybqsr | circle, #4CAF50
%%metro marker: vc_anchor | pill, open

%% Sentieon-accelerated callers in the pathways panel (navy circles).  Single-rail
%% callers (haplotyper, dnascope) show the marker; tnscope spans two rails and
%% renders as a plain interchange (a marker on a spanning rail station is drawn
%% as the interchange bar, not the glyph).
%%metro marker: haplotyper | circle, #1b3a6b
%%metro marker: dnascope | circle, #1b3a6b
%%metro marker: tnscope | circle, #1b3a6b


graph LR
    subgraph preprocessing [Pre-processing]
        ubam_in[ ]
        spring_in[ ]
        fastq_in[ ]
        convert[convert]
        fastqc[FastQC]
        umi[UMI]
        fastp[FastP]
        bbsplit[BBsplit]
        mapping[mapping]
        bam_convert[convert]
        markduplicates[markduplicates]
        mosdepth[mosdepth, samtools]
        prepare_recal[prepare recalibration]
        applybqsr[applybqsr]
        mosdepth_qc[mosdepth, samtools]
        ngscheckmate[NGSCheckmate]
        mapped_out[ ]
        samtools_out[ ]
        recalprep_out[ ]
        recal_out[ ]

        ubam_in -->|core| convert
        spring_in -->|core| convert
        fastq_in -->|core| fastqc
        convert -->|core| fastqc
        fastqc -->|core| umi
        umi -->|core| fastp
        fastp -->|core| bbsplit
        bbsplit -->|core| mapping
        mapping -->|core| bam_convert
        mapping -->|core| markduplicates
        bam_convert -->|core| mosdepth
        markduplicates -->|core| mosdepth
        mosdepth -->|core| prepare_recal
        prepare_recal -->|core| applybqsr
        applybqsr -->|core| mosdepth_qc
        mosdepth_qc -->|core| ngscheckmate

        mapping -->|core| mapped_out
        mosdepth -->|core| samtools_out
        prepare_recal -->|core| recalprep_out
        applybqsr -->|core| recal_out
    end

    subgraph variantcalling [Variant calling]
        vc_anchor[variant calling]
        bcftools[bcftools]
        samtools_vc[samtools]
        varlociraptor[Varlociraptor]
        finalise[finalise]
        normalise[normalise]
        consensus[consensus]
        _vc_merge[ ]
        vcf_vc[ ]

        vc_anchor -->|core| bcftools
        bcftools -->|core| samtools_vc
        samtools_vc -->|core| varlociraptor
        samtools_vc -->|core| finalise
        finalise -->|core| normalise
        normalise -->|core| consensus
        varlociraptor -->|core| _vc_merge
        consensus -->|core| _vc_merge
        _vc_merge -->|core| vcf_vc
    end

    subgraph annotation [Annotation]
        snpeff[snpEff]
        ensemblvep[ensemblVEP]
        bcftools_annotate[bcftools annotate]
        multiqc[MultiQC]
        vcf_ann[ ]

        snpeff -->|core| ensemblvep
        ensemblvep -->|core| bcftools_annotate
        bcftools_annotate -->|core| multiqc
        multiqc -->|core| vcf_ann
    end

    subgraph calling [Example analysis pathways]
        cram_call[ ]
        deepvariant[DeepVariant]
        freebayes[FreeBayes]
        haplotypecaller[HaplotypeCaller]
        haplotyper[Sentieon Haplotyper]
        dnascope[Sentieon DNAscope]
        tnscope[Sentieon TNscope]
        lofreq[LoFreq]
        muse[MuSE]
        mpileup[mpileup]
        mutect2[Mutect2]
        strelka2[Strelka2]
        indexcov[indexcov]
        manta[Manta]
        tiddit[TIDDIT]
        ascat[ASCAT]
        controlfreec[Control-FREEC]
        cnvkit[CNVkit]
        msisensor2[MSIsensor2]
        msisensorpro[MSIsensor-pro]
        out[ ]

        %% Germline route (top rail): deepvariant, haplotypecaller, haplotyper,
        %% dnascope are germline-only; freebayes/mpileup/strelka2/manta/tiddit/
        %% cnvkit/indexcov are shared.
        cram_call -->|germline| deepvariant
        deepvariant -->|germline| freebayes
        freebayes -->|germline| haplotypecaller
        haplotypecaller -->|germline| haplotyper
        haplotyper -->|germline| dnascope
        dnascope -->|germline| mpileup
        mpileup -->|germline| strelka2
        strelka2 -->|germline| indexcov
        indexcov -->|germline| manta
        manta -->|germline| tiddit
        tiddit -->|germline| cnvkit
        cnvkit -->|germline| out

        %% Tumour-only route (middle rail): tnscope, lofreq, mutect2, msisensor2
        %% join here; mpileup/indexcov run tumour but not the combined pair.
        cram_call -->|tumor_only| freebayes
        freebayes -->|tumor_only| tnscope
        tnscope -->|tumor_only| lofreq
        lofreq -->|tumor_only| mpileup
        mpileup -->|tumor_only| mutect2
        mutect2 -->|tumor_only| indexcov
        indexcov -->|tumor_only| manta
        manta -->|tumor_only| tiddit
        tiddit -->|tumor_only| controlfreec
        controlfreec -->|tumor_only| cnvkit
        cnvkit -->|tumor_only| msisensor2
        msisensor2 -->|tumor_only| out

        %% Tumour-normal pair route (bottom rail): muse, ascat, msisensorpro are
        %% combined-only; strelka2 runs germline + combined (not tumour-only).
        cram_call -->|pair_n,pair_t| freebayes
        freebayes -->|pair_n,pair_t| tnscope
        tnscope -->|pair_n,pair_t| muse
        muse -->|pair_n,pair_t| mutect2
        mutect2 -->|pair_n,pair_t| strelka2
        strelka2 -->|pair_n,pair_t| manta
        manta -->|pair_n,pair_t| tiddit
        tiddit -->|pair_n,pair_t| ascat
        ascat -->|pair_n,pair_t| controlfreec
        controlfreec -->|pair_n,pair_t| cnvkit
        cnvkit -->|pair_n,pair_t| msisensorpro
        msisensorpro -->|pair_n,pair_t| out
    end

    %% Inter-section: core workflow flows through the top three sections.
    ngscheckmate -->|core| vc_anchor
    _vc_merge -->|core| snpeff

CLI command

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

Rendered map

nf-core/seqinspector

Dedicated QC-only pipeline for sequencing data, running FASTQ, BAM, and run-folder QC tools in parallel and aggregating everything into a MultiQC report. GitHub

Mermaid source

%%metro title: nf-core/seqinspector
%%metro style: dark
%%metro logo: examples/showcase/nf-core-seqinspector_logo_light.png | examples/showcase/nf-core-seqinspector_logo_dark.png

%%metro line: run_folder | Run Folder | #1f77b4
%%metro line: fastq_files | FASTQ Files | #ff7f0e
%%metro line: bam_files | BAM Files | #24B064

%%metro file: fastq_in | FASTQ | | banner
%%metro dir: rundir_in | RUNDIR
%%metro file: multiqc | HTML | | banner
%%metro center_ports: true
%%metro compact_offsets: true
%%metro legend: bl
%%metro grid: fastq_files | 0,0,2
%%metro grid: run_folder | 1,0
%%metro grid: bam_files | 1,1
%%metro grid: multiqc | 2,0,2

graph LR
    subgraph fastq_files [FASTQ Files]
        fastq_in[ ]

        bbmap[BBMap Clumpify]
        fastp[FastP]
        fastqc[FASTQC]
        fastqe[FASTQE]
        fastqscreen[FastQ Screen]
        fq_lint[FQ Lint]
        kraken2[Kraken2]
        krona[Krona]
        seqfu[SeqFu Stats]
        seqkit[SeqKit Stats]
        seqtk[Seqtk sample]
        sequali[Sequali]
        toulligqc[ToulligQC]

        fastq_in -->|fastq_files| seqtk

        seqtk -->|fastq_files| kraken2
        kraken2 -->|fastq_files| krona

        subgraph bam_files [BAM Files]
            bwamem2[BWAmem2]

            picardhs[Picard collecthsmetrics]
            picardmultiple[Picard collectmultiplemetrics]
            riker[Riker multi]

            bwamem2 -->|bam_files| picardhs
            bwamem2 -->|bam_files| picardmultiple
            bwamem2 -->|bam_files| riker
        end

        seqtk -->|fastq_files| bbmap
        seqtk -->|fastq_files| bwamem2
        seqtk -->|fastq_files| fastp
        seqtk -->|fastq_files| fastqc
        seqtk -->|fastq_files| fastqe
        seqtk -->|fastq_files| fastqscreen
        seqtk -->|fastq_files| fq_lint
        seqtk -->|fastq_files| seqfu
        seqtk -->|fastq_files| seqkit
        seqtk -->|fastq_files| sequali
        seqtk -->|fastq_files| toulligqc
    end

    subgraph run_folder [Run Folder]
        rundir_in[ ]

        checkqc[CheckQC]
        rundirparser[Rundirparser]

        rundir_in -->|run_folder| checkqc
        rundir_in -->|run_folder| rundirparser
    end

    subgraph multiqc [MultiQC]
        multiqc[MultiQC]

        bbmap -->|fastq_files| multiqc
        checkqc -->|run_folder| multiqc
        fastp -->|fastq_files| multiqc
        fastqc -->|fastq_files| multiqc
        fastqe -->|fastq_files| multiqc
        fastqscreen -->|fastq_files| multiqc
        fq_lint -->|fastq_files| multiqc
        krona -->|fastq_files| multiqc
        picardhs -->|bam_files| multiqc
        picardmultiple -->|bam_files| multiqc
        riker -->|bam_files| multiqc
        rundirparser -->|run_folder| multiqc
        seqfu -->|fastq_files| multiqc
        seqkit -->|fastq_files| multiqc
        sequali -->|fastq_files| multiqc
        toulligqc -->|fastq_files| multiqc
    end

CLI command

nf-metro render examples/showcase/seqinspector.mmd -o seqinspector.svg

Rendered map

nf-core/variantbenchmarking

Benchmarking of variant callers against truth sets with Truvari, hap.py, RTGtools, and more. GitHub

Mermaid source

%%metro title: nf-core/variantbenchmarking
%%metro style: dark
%%metro line_order: span
%%metro legend: bl
%%metro compact_offsets: true
%%metro grid: inputs | 0,0
%%metro grid: preprocess | 1,0
%%metro grid: normalization | 2,0
%%metro grid: filtering | 3,0
%%metro grid: stats | 4,0
%%metro grid: benchmarking | 3,1
%%metro grid: ensembl_truth | 4,1
%%metro grid: output_processing | 1,1,1,2
%%metro file: ref_genome_file | FASTA
%%metro file: truth_vcf_file | VCF
%%metro file: regions_bed_file | BED
%%metro file: targets_bed_file | BED
%%metro file: samplesheet_file | TSV
%%metro file: snv_stats_out | TSV
%%metro file: sv_stats_out | TSV
%%metro file: merged_csvs_out | CSV
%%metro file: html_report_out | HTML
%%metro file: multiqc_out | HTML
%%metro line: truth | Truth Preprocessing | #4CAF50
%%metro line: test | Test Preprocessing | #ff9800
%%metro line: sv_cnv | SV/CNV Benchmarking | #E53935
%%metro line: snv_indel | SNV/INDEL Benchmarking | #AB47BC
%%metro line: concordance | Concordance | #FFB300
%%metro line: intersection | Intersection | #26A69A
%%metro line: output | Output Processing | #03A9F4

graph LR
    subgraph inputs [Inputs]
        %%metro exit: right | truth, test
        ref_genome_file[ ]
        ref_genome[Reference Genome]
        truth_vcf_file[ ]
        truth_vcf[Truth VCF]
        regions_bed_file[ ]
        regions_bed[Regions BED]
        targets_bed_file[ ]
        targets_bed[Targets BED]
        samplesheet_file[ ]
        samplesheet[Samplesheet]
        _inputs_hub[hidden]

        ref_genome_file -->|truth| ref_genome
        truth_vcf_file -->|truth| truth_vcf
        regions_bed_file -->|truth| regions_bed
        targets_bed_file -->|truth| targets_bed
        samplesheet_file -->|test| samplesheet
        ref_genome -->|truth| _inputs_hub
        truth_vcf -->|truth| _inputs_hub
        regions_bed -->|truth| _inputs_hub
        targets_bed -->|truth| _inputs_hub
        samplesheet -->|test| _inputs_hub
    end

    subgraph preprocess ["Preprocessing (Optional)"]
        %%metro entry: left | truth, test
        %%metro exit: right | truth, test
        subsample[Subsample]
        liftover["Liftover\n(Picard, UCSC)"]
        subsample -->|test| liftover
    end

    subgraph normalization ["Variant Normalization (Optional)"]
        %%metro entry: left | truth, test
        %%metro exit: right | truth, test
        sv_processing[SV\nProcessing]
        var_norm[Variant\nNormalization]
        sv_processing -->|test| var_norm
    end

    subgraph filtering ["Variant Filtering (Optional)"]
        %%metro entry: left | test
        %%metro exit: right | test
        filter_contigs[Filter\nContigs]
        bcftools_filter[bcftools\nfilter]
        survivor_filter[SURVIVOR\nfilter]
        filter_contigs -->|test| bcftools_filter
        filter_contigs -->|test| survivor_filter
    end

    subgraph ensembl_truth [Ensembl Truth]
        %%metro direction: TB
        %%metro entry: top | test
        %%metro exit: left | truth
        _ensembl_hub[hidden]
        survivor_merge[SURVIVOR\nmerge]
        bcftools_merge[bcftools\nmerge]
        consensus_filter[Consensus\nFilter]
        _ensembl_hub -->|test| survivor_merge
        _ensembl_hub -->|test| bcftools_merge
        survivor_merge -->|test| consensus_filter
        bcftools_merge -->|test| consensus_filter
    end

    subgraph benchmarking [Benchmarking]
        %%metro direction: RL
        %%metro entry: top | test, truth
        %%metro entry: right | test, truth
        bench_hub[ ]
        truvari[Truvari]
        rtg_vcfeval[RTGtools vcfeval]
        svanalyzer[SVanalyzer]
        rtg_bndeval[RTGtools bndeval]
        happy[hap.py]
        wittyer[wittyer]
        sompy[som.py]
        intersection_tool[Intersection]
        gatk4_conc[GATK4 Concordance]
        bench_hub -->|sv_cnv| truvari
        bench_hub -->|snv_indel| rtg_vcfeval
        bench_hub -->|sv_cnv| svanalyzer
        bench_hub -->|sv_cnv| rtg_bndeval
        bench_hub -->|snv_indel| happy
        bench_hub -->|sv_cnv| wittyer
        bench_hub -->|snv_indel| sompy
        bench_hub -->|intersection| intersection_tool
        bench_hub -->|concordance| gatk4_conc
        %%metro exit: left | sv_cnv, snv_indel, concordance, intersection
    end

    subgraph output_processing [Output Processing]
        %%metro direction: RL
        %%metro entry: right | sv_cnv, snv_indel, concordance, intersection
        results_hub[ ]
        merge_res[Merge\nTP/FP/FN]
        vcf2csv[VCF to\nCSV]
        sum_stats[Summary\nStats]
        plots[Plots]
        datavzrd_tool[datavzrd]
        merged_csvs[Merged\nCSVs]
        merged_csvs_out[ ]
        bench_summaries[Benchmarking\nSummaries]
        html_report[HTML\nReport]
        html_report_out[ ]
        multiqc[MultiQC\nReport]
        multiqc_out[ ]

        results_hub -->|output| merge_res
        merge_res -->|output| vcf2csv
        results_hub -->|output| sum_stats
        sum_stats -->|output| plots
        sum_stats -->|output| datavzrd_tool
        vcf2csv -->|output| plots
        vcf2csv -->|output| merged_csvs
        merged_csvs -->|output| merged_csvs_out
        results_hub -->|output| bench_summaries
        datavzrd_tool -->|output| html_report
        html_report -->|output| html_report_out
        sum_stats -->|output| multiqc
        bench_summaries -->|output| multiqc
        plots -->|output| multiqc
        multiqc -->|output| multiqc_out
    end

    subgraph stats [Variant Statistics]
        %%metro entry: left | test
        %%metro exit: right | test, output
        bcftools_stats[bcftools\nstats]
        survivor_stats[SURVIVOR\nstats]
        snv_stats[SNV stats]
        sv_stats[SV stats]
        snv_stats_out[ ]
        sv_stats_out[ ]
        bcftools_stats -->|output| snv_stats
        survivor_stats -->|output| sv_stats
        snv_stats -->|output| snv_stats_out
        sv_stats -->|output| sv_stats_out
    end

    %% Section 1 -> 2: test through Subsample, truth to Liftover
    _inputs_hub -->|test| subsample
    _inputs_hub -->|truth| liftover
    %% Section 2 -> 3: test to SV Processing, truth to Var Norm
    liftover -->|test| sv_processing
    liftover -->|truth| var_norm
    %% Section 1 -> 3 (bypass section 2)
    _inputs_hub -->|test| sv_processing
    _inputs_hub -->|truth| var_norm
    %% Section 3 -> 4
    var_norm -->|test| filter_contigs
    %% Section 4 -> 5: each filter to its corresponding stats
    bcftools_filter -->|test| bcftools_stats
    survivor_filter -->|test| survivor_stats
    %% Section 4 -> Ensembl Truth
    bcftools_filter -->|test| _ensembl_hub
    survivor_filter -->|test| _ensembl_hub
    %% Multiple sections -> Benchmarking
    filter_contigs -->|test| bench_hub
    var_norm -->|truth| bench_hub
    consensus_filter -->|truth| bench_hub
    %% Benchmarking -> Output Processing
    truvari -->|sv_cnv| results_hub
    svanalyzer -->|sv_cnv| results_hub
    rtg_bndeval -->|sv_cnv| results_hub
    wittyer -->|sv_cnv| results_hub
    rtg_vcfeval -->|snv_indel| results_hub
    happy -->|snv_indel| results_hub
    sompy -->|snv_indel| results_hub
    intersection_tool -->|intersection| results_hub
    gatk4_conc -->|concordance| results_hub

CLI command

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

Rendered map

nf-core/variantprioritization

Somatic and germline variant prioritization using PCGR and CPSR. GitHub

Mermaid source

%%metro title: nf-core/variantprioritization
%%metro file: cna_in | CNA
%%metro file: vcf_in | VCF
%%metro file: report_pcgr | HTML
%%metro file: report_cpsr | HTML
%%metro line: somatic | Somatic | #4CAF50
%%metro line: germline | Germline | #9923A0
%%metro line: reference | Reference | #2196F3

graph LR

    subgraph preprocessing [Pre-processing of vcf files]
        vcf_in[ ]
        tabix[tabix]
        bcftools_norm[bcftools/norm]
        bcftools_filter[bcftools/filter]

        vcf_in -->|somatic,germline| tabix
        tabix -->|somatic,germline| bcftools_norm
        bcftools_norm -->|somatic,germline| bcftools_filter
    end

    subgraph format_files [Prepare files for PCGR]
        reformat_vcf[Reformat VCF]
        intersect[Intersect VCF]
        prepare_pcgr[Prepare VCF]
        cna_in[ ]
        reformat_cna[Reformat CNA]

        reformat_vcf -->|somatic| intersect
        reformat_vcf -->|somatic| prepare_pcgr
        intersect -->|somatic| prepare_pcgr
        cna_in -->|somatic| reformat_cna
    end

    subgraph get_reference [Reference]
        get_pcgr[PCGR DB]
        get_vep[VEP Cache]
    end

    subgraph run_pcgr [PCGR]
        pcgr[PCGR]
        report_pcgr[ ]

        pcgr -->|somatic| report_pcgr
    end

    subgraph run_cpsr [CPSR]
        cpsr[CPSR]
        report_cpsr[ ]

        cpsr -->|germline| report_cpsr
    end

    %% Inter-section edges
    get_pcgr -->|reference| cpsr
    get_vep -->|reference| cpsr
    bcftools_filter -->|germline| cpsr
    bcftools_filter -->|somatic| reformat_vcf
    reformat_cna -->|somatic| pcgr
    prepare_pcgr -->|somatic| pcgr
    get_pcgr -->|reference| pcgr
    get_vep -->|reference| pcgr

CLI command

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

Rendered map