Using Galaxy webhooks to nudge users toward better tools

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. 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.

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.