Add pipeline metro map - #83
Merged
Merged
Conversation
Add nf-metro diagram showing the full rnadnavar pipeline flow: - 3 lines: DNA (blue), RNA (red), Realignment (gold) - 6 sections: Pre-processing, GATK Preprocessing, Variant Calling, Normalization & Annotation, Consensus & Filtering, Realignment & RNA Filtering - 45 stations covering all pipeline tools from FastQC through MultiQC - SVG rendered with nf-core theme and embedded fonts
Triggers on changes to assets/metro_map.mmd: - On push to dev/master: re-renders SVG and auto-commits if changed - On PR: warns if the SVG is stale (will be updated on merge)
- Remove docs/images/rnadnavar_schemav3.png - Update README.md to reference assets/metro_map.svg
|
fold-threshold 18 was too tight for the 'realign' section's bundle routing. 20 gives the router enough room while keeping the map compact.
Author
|
screenshot of the new readme: 
|
adamrtalbot
commented
Jun 30, 2026
Mutect2, Strelka2, and SAGE run in parallel (not serially) in the pipeline. Updated the metro map to fan out from a fork node and converge at a join node before normalization.
Rendered at 2011px wide (down from 3104px) to fit a single screen.
Member
|
I love it <3 |
adamrtalbot
marked this pull request as draft
June 30, 2026 11:33
Author
|
The idea is solid but the mermaid is a bit mangled - converting to draft while I fix. [update] Done |
This was referenced Jun 30, 2026
Split the oversized Consensus/Realignment section into Consensus & Filtering, Realignment, and Reporting so nf-metro auto-folds the chain into a horseshoe (top row L->R, bottom row R->L) that fits a vertical README. Show Mutect2/Strelka2/SAGE as parallel branches. Render at --fold-threshold 15. Generated by Claude Code
adamrtalbot
marked this pull request as ready for review
June 30, 2026 12:32
Collaborator
|
@adamrtalbot this is AMAZING!!! thank you, looking beautiful. I am doing some edits, will get back to you. |
This was referenced Jun 30, 2026
Member
|
Had a go at some improvements and bug fixes - opened #87 against this branch. Folds the map into a compact layout, fixes the logo path, makes it light/dark adaptive. Note it relies on a few nf-metro fixes that'll be in the next release; the committed SVG is pre-rendered so the README's fine now, and CI re-render will match once nf-metro updates. |
pinin4fjords
reviewed
Jul 1, 2026
Collaborator
|
This is WOW!! I didn't have time to work on this until now. Thank you both looks great. I just changed a couple of things to dashed so it is clear what is optional and what is the main pipeline. |
RaqManzano
reviewed
Jul 23, 2026
RaqManzano
left a comment
RaqManzano
left a comment
Collaborator
There was a problem hiding this comment.
LGTM
I guess we are just waiting for a new release of nf-metro and the tests should work?
Update logo path from non-existent examples/ to docs/images/. nf-metro 1.1.0 errors on missing logo where 1.0.0 ignored it. Generated by Claude Code
Author
My fault, should be fixed now. Check the metro map and make sure you like it. |
RaqManzano
approved these changes
Jul 23, 2026
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
4 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
Adds an nf-metro diagram visualizing the full rnadnavar pipeline flow, replaces the old PNG in the README, and adds CI automation to keep the SVG in sync.
Details
The original image didn't look very good on dark mode:
So I decided to try @pinin4fjords's nf-metro and refine it a bit. This should also be straightforward to maintain from a mermaid diagram (code) instead of an image.
assets/metro_map.mmd(nf-metro Mermaid-extended format)assets/metro_map.svg(nf-core dark theme, embedded fonts)Changes
assets/metro_map.mmd— new nf-metro source fileassets/metro_map.svg— rendered SVG (nf-core dark theme, embedded fonts)README.md— replaceddocs/images/rnadnavar_schemav3.pngreference withassets/metro_map.svgdocs/images/rnadnavar_schemav3.png(superseded).github/workflows/metro-map.yml— CI workflow to auto-render the SVG on changesCI Automation (
.github/workflows/metro-map.yml)dev/master: re-renders the SVG fromassets/metro_map.mmdand auto-commits if it changed (with[skip ci])astral-sh/setup-uv+uv tool install nf-metrofor fast, reproducible installsPipeline coverage
6 sections across 2 rows, 45 stations, 75 edges:
Rendering