Add Galaxy workflow visualization skill and SVG diagrams for featured workflows#1097
Merged
mvdbeek merged 17 commits intogalaxyproject:mainfrom Feb 12, 2026
Merged
Add Galaxy workflow visualization skill and SVG diagrams for featured workflows#1097mvdbeek merged 17 commits intogalaxyproject:mainfrom
mvdbeek merged 17 commits intogalaxyproject:mainfrom
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Claude Code skill that generates Galaxy-branded SVG workflow visualizations matching the workflow editor's visual style. Includes bezier connection math, node card templates, and examples for ChIP-seq, RNA-seq, and end-to-end DE workflows.
Updated SKILL.md with proper color mapping: - Gold (#ffd700) for data inputs (FASTQs, GTF, sample sheets) - Blue (#25537b) for processing/analysis steps - Orange (#f97316) for workflow outputs - Green (#10b981) for QC/reports Added Input Node Template and Legend Template sections. Regenerated all three example SVGs from scratch using the skill.
Generated Galaxy-branded SVG visualizations for 6 workflows: - atacseq (featured) - rnaseq-de-filtering-plotting - cgmlst-bacterial-genome - sra-manifest-to-concatenated-fastqs - Purge-duplicate-contigs-VGP6 - Purging-duplicates-one-haplotype-VGP6b Updated manifest script to load diagram_svg field from *-diagram.svg files. Updated WorkflowContent.vue to display SVG overview above Mermaid diagrams.
- Add workflow name as h1 at top of diagram tab - h2 "Workflow Overview" for SVG visualization - h2 "Step Diagram" for Mermaid content - Strip redundant headings from markdown content - Add SVG diagrams for chipseq-pe and rnaseq-pe (featured workflows)
dannon
changed the title
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Color Scheme DiscussionI've been thinking about standardizing the node colors for these workflow visualizations. We want something consistent and semantically meaningful. Here's what we have currently vs. a proposed alternative:
Rationale for proposed change
Questions for reviewers
Would love input before we generate diagrams for more workflows! |
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These are really cool! I'll render a few tomorrow, the new proposal makes sense to me but I'll have to compare a few examples side by side. |
ChIP-seq SR, CUT&RUN, average bigwig, three consensus peaks variants, and four Hi-C/CHi-C processing workflows.
…epeatmasking, and data fetching RNA-seq SR, BREW3R 3'UTR extension, GOseq enrichment analysis, short-read QC/trimming, RepeatMasking, and parallel accession download.
All QIIME2 import/denoising/downstream variants, DADA2 paired-end, and MGnify amplicon pipeline workflows (QC SE/PE, ITS, rRNA prediction, complete pipeline, summary tables, rank abundance, MAPseq-to-ampvis2).
AMR gene detection, bacterial genome annotation, and post-assembly quality/contamination control workflows.
Flye assembly, long-read polishing, bacterial genome assembly, raw-read QC, and annotation pipelines (Braker3, Helixer, Maker, functional annotation, lncRNA annotation).
Protein-ligand parameterization, fragment-based docking, GROMACS dcTMD and MMGBSA, GC-MS with metaMS, LC-MS with XCMS, MFAssignR molecular formula assignment, and QCxMS spectra prediction.
Fluorescence nuclei segmentation/counting, multiplex tissue microarray analysis, and end-to-end tissue microarray analysis.
Host contamination removal (short/long reads), metagenomic AMR analysis, genes catalogue, MAGs generation, Krona taxonomy profiling, and PathoGFAIR suite (nanopore preprocessing, gene-based/allele-based pathogen ID, samples aggregation and visualisation).
OpenMS MetaProSIP stable isotope analysis and the full ClinicalMP suite (database generation, discovery, quantitation, data interpretation, verification).
SE/PE Illumina WGS, PE ARTIC ivar analysis, PE ARTIC variant calling, ONT ARTIC, consensus from variation, and variation reporting.
baredSC 1D/2D log-normalized, FASTQ-to-matrix 10X v3 and CellPlex, Velocyto (filtered barcodes and bundled), pseudobulk edgeR, and Scanpy preprocessing/clustering.
Generic WGS PE variant calling, haploid variant calling, variation reporting, non-segmented viral variant calling, influenza consensus and subtyping, and pox virus amplicon half-genome.
Full VGP pipeline: mitogenome assembly (VGP0), k-mer profiling HiFi (VGP1) and trio (VGP2), HiFi-only assembly (VGP3), HiFi+Hi-C phasing (VGP4), HiFi+trio phasing (VGP5), BioNano scaffolding (VGP7), Hi-C scaffolding (VGP8), decontamination (VGP9), Nx/size plots, and Hi-C contact maps for manual curation.
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Attention: deployment cancelled! https://github.com/galaxyproject/iwc/actions/runs/21951050708 |
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Summary
Adds a Claude Code skill for generating Galaxy-branded workflow visualization SVGs, plus SVG diagrams for featured and recently updated workflows with website integration.
Skill
.claude/skills/galaxy-workflow-viz/Node Color Semantics
SVG Diagrams Generated
Featured workflows (hero cards):
Recently updated workflows:
Website Integration
workflow_manifest.pyto load*-diagram.svgfiles intodiagram_svgfieldWorkflowContent.vueto display SVG overview above Mermaid diagramsExample Visualizations
ChIP-seq PE
RNA-seq PE
Future Plans
We'll continue generating these visualizations for all IWC workflows. The skill enables LLM-assisted generation with human review for quality.
We also need to work on the layout a little -- see ATAC-seq:
Test plan