Simon Pearce
Simon Pearce
~~Hmm, I've tried to build the feature/codec branch and I still get the same for the example sam file above. `java -jar target/scala-2.13/fgbio-2.5.22-61db498-SNAPSHOT.jar GroupReadsByUmi --input test.sam --output out.sam -f hist.txt...
Ignore that, it seems to be working for me.
Just to update, the `feature/codec` branch is resolving this issue for me. Do you have a timeline to release this?
Yep, lets give it a go, we wanted to move to that anyway.
Yep, I think we give this a go and revert if everything breaks.
> > Maybe there is a more elegant way? > > I think we could write a lib function for this, either in this repo or the nf-test/utils plugin. >...
So, do we want to deprecate this?
> I don't know if we have a deprecation procedure do we? Oh James, [I thought you knew the guidelines](https://nf-co.re/docs/guidelines/components/module_deprecation#deprecating-a-module) 😉.
[Looks like we have 3 modules and a subworkflow deprecated so far](https://github.com/search?q=repo%3Anf-core%2Fmodules+has+been+deprecated&type=code).
Added a message. I don't know what happens to the tests at that point, but they seem to be fine for the other modules so maybe they just ignore the...