I'm actually going to encourage a little caution here.
As a pipeline maintainer with a community to think about, I have more to consider than the raw speed of any given tool. I need confidence in both the fidelity of a rewrite and its long-term sustainability and maintenance. So I'd gently discourage any lone wolves from jumping in and submitting rewrites unprompted.
That said, here's where things stand:
- RustQC, by @Phil Ewels with Seqera behind it, is already included as an experimental option.
- STAR alignment - the most expensive part of the pipeline — is being rewritten by some of the top experts in the field, so I'm looking forward to that one with confidence.
- TrimGalore - as you can see above, @Felix Krueger is already on it. As the original author, he's uniquely placed to match the existing behaviour and support the tool long-term - exactly the kind of continuity I need.
For anything remaining, I'm not sure the performance payoff is compelling enough to justify a rewrite by anyone other than the original authors themselves. But the interest is appreciated!