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Rnaseq Sections

Gallery / Getting Started

Same pipeline with manual `%%metro grid:` overrides and file markers, showing how explicit directives can fine-tune placement.

Mermaid source
examples/rnaseq_sections.mmd
%%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 file: fastq_in | FASTQ
%%metro file: report_final | HTML
%%metro file: report_quant | HTML
%%metro file: report_bowtie2 | HTML
%%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: bowtie2_salmon | Aligner: Bowtie2, Quantification: Salmon | #ff8c00
%%metro line: pseudo_salmon | Pseudo-aligner: Salmon, Quantification: Salmon | #e63946
%%metro line: pseudo_kallisto | Pseudo-aligner: Kallisto, Quantification: Kallisto | #7b2d3b
%%metro legend: bl


graph LR
    subgraph preprocessing [Pre-processing]
        %%metro exit: right | star_salmon, star_rsem, hisat2, bowtie2_salmon
        %%metro exit: bottom | pseudo_salmon, pseudo_kallisto
        fastq_in[ ]
        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]
        ribodetector[RiboDetector]
        fastqc_filtered[FastQC]


        fastq_in -->|pseudo_salmon,pseudo_kallisto,star_salmon,star_rsem,hisat2,bowtie2_salmon| cat_fastq
        cat_fastq -->|pseudo_salmon,pseudo_kallisto,star_salmon,star_rsem,hisat2,bowtie2_salmon| fastqc_raw
        fastqc_raw -->|pseudo_salmon,pseudo_kallisto,star_salmon,star_rsem,hisat2,bowtie2_salmon| infer_strandedness
        infer_strandedness -->|pseudo_salmon,pseudo_kallisto,star_salmon,star_rsem,hisat2,bowtie2_salmon| umi_tools_extract


        umi_tools_extract -->|pseudo_salmon,pseudo_kallisto,star_salmon,star_rsem,hisat2,bowtie2_salmon| fastp
        umi_tools_extract -->|pseudo_salmon,pseudo_kallisto,star_salmon,star_rsem,hisat2,bowtie2_salmon| trimgalore
        fastp -->|pseudo_salmon,pseudo_kallisto,star_salmon,star_rsem,hisat2,bowtie2_salmon| fastqc_trimmed
        trimgalore -->|pseudo_salmon,pseudo_kallisto,star_salmon,star_rsem,hisat2,bowtie2_salmon| fastqc_trimmed


        fastqc_trimmed -->|pseudo_salmon,pseudo_kallisto,star_salmon,star_rsem,hisat2,bowtie2_salmon| bbsplit
        fastqc_trimmed -->|pseudo_salmon,pseudo_kallisto,star_salmon,star_rsem,hisat2,bowtie2_salmon| sortmerna
        fastqc_trimmed -->|pseudo_salmon,pseudo_kallisto,star_salmon,star_rsem,hisat2,bowtie2_salmon| ribodetector
        bbsplit -->|pseudo_salmon,pseudo_kallisto,star_salmon,star_rsem,hisat2,bowtie2_salmon| fastqc_filtered
        sortmerna -->|pseudo_salmon,pseudo_kallisto,star_salmon,star_rsem,hisat2,bowtie2_salmon| fastqc_filtered
        ribodetector -->|pseudo_salmon,pseudo_kallisto,star_salmon,star_rsem,hisat2,bowtie2_salmon| fastqc_filtered
    end


    subgraph genome_align [Genome alignment & quantification]
        %%metro entry: left | star_salmon, star_rsem, hisat2, bowtie2_salmon
        %%metro exit: right | star_salmon, star_rsem
        %%metro exit: right | hisat2
        star[STAR]
        hisat2_align[HISAT2]
        bowtie2_align[Bowtie2]
        rsem[RSEM]
        salmon_quant[Salmon]
        umi_tools_dedup[UMI-tools Dedup]
        tximport_ga[tximport]
        summarized_exp_ga[Sum. Exp.]
        multiqc_bowtie2[MultiQC]
        report_bowtie2[ ]
        _h1[hidden]
        _h2[hidden]
        _h3[hidden]


        star -->|star_rsem| rsem
        star -->|star_salmon| umi_tools_dedup
        hisat2_align -->|hisat2| umi_tools_dedup
        bowtie2_align -->|bowtie2_salmon| umi_tools_dedup
        umi_tools_dedup -->|star_salmon| salmon_quant
        umi_tools_dedup -->|hisat2| _h1
        _h1 -->|hisat2| _h2
        _h2 -->|hisat2| _h3
        salmon_quant -->|star_salmon| tximport_ga
        rsem -->|star_rsem| tximport_ga
        tximport_ga -->|star_salmon,star_rsem| summarized_exp_ga
        umi_tools_dedup -->|bowtie2_salmon| salmon_quant
        salmon_quant -->|bowtie2_salmon| multiqc_bowtie2
        multiqc_bowtie2 -->|bowtie2_salmon| report_bowtie2
    end


    subgraph pseudo_align [Pseudo-alignment & quantification]
        %%metro entry: left | pseudo_salmon, pseudo_kallisto
        salmon_pseudo[Salmon]
        kallisto[Kallisto]
        tximport_pa[tximport]
        summarized_exp_pa[Sum. Exp.]
        multiqc_quant[MultiQC]
        report_quant[ ]


        salmon_pseudo -->|pseudo_salmon| tximport_pa
        kallisto -->|pseudo_kallisto| tximport_pa
        tximport_pa -->|pseudo_salmon,pseudo_kallisto| summarized_exp_pa
        summarized_exp_pa -->|pseudo_salmon,pseudo_kallisto| multiqc_quant
        multiqc_quant -->|pseudo_salmon,pseudo_kallisto| report_quant
    end


    subgraph postprocessing [Post-processing]
        %%metro direction: TB
        %%metro entry: left | star_salmon, star_rsem, hisat2
        %%metro exit: bottom | star_salmon, star_rsem, hisat2
        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 qc_report [Quality control & reporting]
        %%metro direction: RL
        %%metro entry: top | star_salmon, star_rsem, hisat2
        rseqc[RSeQC]
        preseq[Preseq]
        qualimap[Qualimap]
        dupradar[dupRadar]
        featurecounts[featureCounts]
        deseq2_pca[DESeq2 PCA]
        kraken2[Kraken2/Bracken]
        sylph[Sylph]
        multiqc_final[MultiQC]
        report_final[ ]


        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| featurecounts
        featurecounts -->|star_salmon,star_rsem,hisat2| deseq2_pca
        deseq2_pca -->|star_salmon,star_rsem,hisat2| kraken2
        deseq2_pca -->|star_salmon,star_rsem,hisat2| sylph
        kraken2 -->|star_salmon,star_rsem,hisat2| multiqc_final
        sylph -->|star_salmon,star_rsem,hisat2| multiqc_final
        multiqc_final -->|star_salmon,star_rsem,hisat2| report_final
    end


    %% Inter-section edges
    fastqc_filtered -->|star_salmon,star_rsem| star
    fastqc_filtered -->|hisat2| hisat2_align
    fastqc_filtered -->|bowtie2_salmon| bowtie2_align
    fastqc_filtered -->|pseudo_salmon| salmon_pseudo
    fastqc_filtered -->|pseudo_kallisto| kallisto
    summarized_exp_ga -->|star_salmon,star_rsem| samtools
    _h3 -->|hisat2| samtools
    stringtie -->|star_salmon,star_rsem,hisat2| rseqc
CLI command
Terminal window
nf-metro render examples/rnaseq_sections.mmd -o rnaseq_sections.svg
Rendered map
1 Pre-processing 2 Genome alignment & quantification 3 Pseudo-alignment & quantification 4 Post-processing 5 Quality control & reporting FASTQ HTML HTML HTML STAR SAMtools RSeQC HISAT2 Bowtie2 Salmon Kallisto Cat FASTQ RSEM Picard Preseq UMI-tools Dedup tximport FastQC BEDTools Qualimap Salmon Sum. Exp. Infer Strandedness tximport bedGraphToBigWig dupRadar MultiQC MultiQC UMI-tools Extract Sum. Exp. StringTie featureCounts fastp DESeq2 PCA Trim Galore! FastQC Kraken2/Bracken Sylph BBSplit MultiQC SortMeRNA RiboDetector FastQC Aligner: STAR, Quantification: RSEM Aligner: STAR, Quantification: Salmon (default) Aligner: HISAT2, Quantification: None Aligner: Bowtie2, Quantification: Salmon Pseudo-aligner: Salmon, Quantification: Salmon Pseudo-aligner: Kallisto, Quantification: Kallisto created with nf-metro v1.1.0+dev