nf-core/hlatyping

nf-core pipelines

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

Mermaid source

examples/hlatyping.mmd

%%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