dannon
commented
3 years ago I copied the above notes from the cofest doc -- my 2c is that this is likely best handled as we modularize components. It's on the near term roadmap to publish components (specifically the tool form first, with workflows soon after) as they are untangled from the galaxy client codebase, and then we could simply use the same exact editor component for external rendering.
From gcc cofest 2021 planning doc, thanks @jrr-cpt!
The workflows used in scientific analyses are highly visual and make great (and often necessary) figures in talks and papers. Screenshots seem to be the best way to capture the workflow visual, but it isn’t editable. There is now an option to download an .svg, which is great, but it’s a bit bare bones. I would love to see better figure generation capability for representing workflows outside Galaxy. Key features: ‘Noodle’ coloring options for subpaths within a workflow Direct download (rather than screenshot) if done within Galaxy Editable upon download
For example, in our published paper, we directly represented the workflows in the figures, but added color to represent the ‘subpaths’ for particular data/analyses within a large workflow. Figure 2 of that paper, which was modified from a Galaxy workflow editor screenshot.
This was discussed in the #cofest Slack channel for GCC2021 (Helena Rasche, Marius van den Beek, Cameron Hyde, Jolene Ramsey). Summary here: This is an early version of an external visualizer written by Helena: https://github.com/hexylena/galaxy-workflow-plotter May be better to develop this outside Galaxy, but end-users could be surveyed to determine how widespread the demand would be at help.galaxyproject.org (don’t immediately see any related entries); also may not fit into current priorities Alternative: cytoscape.js can render workflows, and file to do so can be created with gxwf-viz from gxformat2 https://observablehq.com/@mvdbeek/workflow-preview?url=https://gist.githubusercontent[…]/raw/7f62a8ebe576e250ba7d64ed76f4661da708bb8a/cytoscape.json The cytoscape visualization is a bit basic, though it has options for customization. May be a want for 2-3 levels of detail depending on audience. Advantage is also that it’s a community project and not tied to known Galaxy wf editor/export glitches.