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v0.1

2026-02-16 · GitHub release

The initial public release of nf-metro, establishing the core pipeline: parse a Mermaid .mmd file with %%metro directives, compute a metro-map layout, render to SVG.

Auto-inferred section layout

Section titled “Auto-inferred section layout”

The layout engine infers section positions from the graph topology - for most pipelines, no %%metro grid: directives are needed.

Rendered map
1 Pre-processing 2 Genome alignment & quantification 4 Post-processing 3 Pseudo-alignment & quantification 5 Quality control & reporting cat fastq STAR SAMtools RSeQC HISAT2 Salmon Kallisto FastQC RSEM Picard Preseq UMI-tools dedup MultiQC infer strandedness BEDTools Qualimap Salmon UMI-tools extract bedGraphToBigWig dupRadar FastP StringTie DESeq2 PCA Trim Galore! FastQC Kraken2/Bracken BBSplit MultiQC SortMeRNA Aligner: STAR, Quantification: RSEM Aligner: STAR, Quantification: Salmon (default) Aligner: HISAT2, Quantification: None Pseudo-aligner: Salmon, Quantification: Salmon Pseudo-aligner: Kallisto, Quantification: Kallisto created with nf-metro v1.1.0+dev

For cases where the inferred layout doesn’t match your intent, explicit grid positions override the inference:

%%metro grid: preprocessing | 0,0
%%metro grid: alignment     | 1,0
%%metro grid: quantification| 2,0

Animated balls

Section titled “Animated balls”

--animate adds travelling balls that follow each metro line from source to destination:

Terminal window
nf-metro render mypipeline.mmd --animate -o pipeline.svg

File terminus icons

Section titled “File terminus icons”

Stations representing file inputs or outputs carry a small file icon:

node[Output BAM]:::file
Rendered map
File Icons 1 Analysis 2 Reporting FASTQ HTML MultiQC Trimming Alignment Quantification Main Quality Control created with nf-metro v1.1.0+dev

Transparent background for light theme

Section titled “Transparent background for light theme”

%%metro style: light produces an SVG with a transparent background, suitable for light-coloured docs pages.

Building blocks

Section titled “Building blocks”
Rendered map
Simple Pipeline Input Trimming Alignment FastQC Quantification MultiQC Main Quality Control created with nf-metro v1.1.0+dev
Rendered map
Sectioned Pipeline 1 Pre-processing 2 Analysis 3 Reporting Input Alignment MultiQC Trimming Quantification Report FastQC Main Quality Control created with nf-metro v1.1.0+dev
Rendered map
Fan-out Pipeline 1 Pre-processing 2 WGS Analysis 3 WES Analysis 4 Panel Analysis 5 Annotation FastQC BWA-MEM VEP BWA-MEM Minimap2 Trimming GATK HaplotypeCaller Report GATK Mutect2 FreeBayes Whole Genome Whole Exome Targeted Panel created with nf-metro v1.1.0+dev

CI/CD and PyPI publishing

Section titled “CI/CD and PyPI publishing”

GitHub Actions workflows for CI (test + lint) and publishing to PyPI on release, set up from day one.