nf-core/epitopeprediction

nf-core pipelines

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

Mermaid source

examples/epitopeprediction.mmd

%%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