Merge pull request #3848 from bgruening/fastqc-falco

add post about tool deprecation via toolmsg webhook

Author: nsoranzo

content/news/2026-03-13-galaxy-webhooks-tool-deprecations/fastqc-falco-nudges.png

@@ -0,0 +1,62 @@
+---
+title: "Using Galaxy webhooks to nudge users toward better tools"
+date: "2026-03-13"
+tease: "A small tool-form extension can mark legacy tools as deprecated, keep them available for reproducibility, and guide users toward faster and more efficient alternatives."
+tags: [tools, ui-ux, feature, environmental, esg]
+subsites: [all-eu, esg, global]
+main_subsite: eu
+contributions:
+  funding:
+    - eu
+    - eurosciencegateway
+    - elixir-europe
+    - AustralianBioCommons
+---
+
+Galaxy instances accumulate history. That is a strength, but it also creates a familiar problem: 
+Some tools remain scientifically valid and still need to run for old workflows to enable 
+reproducibility, while newer alternatives are often faster, have better defaults or are easier to 
+use. Outright removing the older tool risks breaking reproducibility. Leaving it untouched means 
+users keep selecting them out of habit.
+
+One practical answer is a soft deprecation layer in the Galaxy tool form itself.
+
+Galaxy already supports site-specific UI extensions through [webhooks](https://docs.galaxyproject.org/en/master/admin/webhooks.html). The same pattern can be used to add contextual information to 
+specific tools. When a user opens an older (still functional) tool, Galaxy can display a short 
+notice explaining that the tool is retained for compatibility, why it is no longer the preferred 
+choice, and which replacement tool should be used instead.
+
+We want to: preserve execution, but improve defaults.
+
+The `FastQC` to `Falco` transition on the European Galaxy server is a good example. `FastQC` is a quality control tool for high-throughput sequence data which has 
+been executed more than two million times over the years and is still deeply embedded in many 
+sequencing workflows. But `Falco`, published in 2021 as a reimplementation of `FastQC`, is roughly 
+three times more efficient. When `Falco` first appeared on the European Galaxy server in June 2024, 
+uptake was limited. Starting in September 2024, we began nudging users more actively. In 
+the `FastQC` interface, in search results, and in training materials. The result was `Falco` reached 158,748 runs, about 29% of `FastQC`'s 546,369 runs in the same time window.
+
+![FastQC to Falco nudges shown in the tool interface, search results, and training material](./fastqc-falco-nudges.png)
+
+These images show the three intervention points together: a notice inside the old tool form, a hint in search results, and updated training content that is using the more efficient tool.
+
+With a webhook-backed tool-form extension, the message can be simple and local to the instance:
+
+- This tool is still available for compatibility and reuse
+- This tool is no longer the recommended default for new analyses
+- We recomment a replacement
+- Here is why the replacement is better: faster runtime, lower resource use, better maintenance status, or improved interoperability
+- Here is a direct link to open the alternative tool or the relevant training material
+
+This approach is intentionally lightweight. It does not require to fork tools, remove wrappers, or 
+invalidate existing workflows. It allows each Galaxy server to maintain a small registry of additional tool annotation mappings and display them only where they matter.
+
+Soft deprecation helps us reduce wasted CPU time, memory, and 
+job queueing time without forcing abrupt migrations. It also creates a transparent path for 
+community tool curation. A tool can continue to exist for provenance and backward compatibility, while the interface tells users clearly that the community has moved on.
+
+`FastQC` and `Falco` show why this matters. Many users were not looking for a new quality-control 
+tool, they were simply opening the tool they already knew and that is cited in throusands of 
+papers. A small information banner changed that behaviour. Extending the tool form with 
+webhook-driven deprecation notices gives Galaxy administrators a practical way to repeat that 
+success for other pairs of tools, whether the motivation is performance, sustainability, 
+maintenance, or a better user experience.