Júlia Mir Pedrol
Júlia Mir Pedrol
Hello! ⚠️ The `nf-validation` plugin will have soon a new release (v2.0) which has breaking changes. This will break the usage of all pipelines that don't pin the version of...
What is the content of `user.config`?
What is happening here is that files have to be staged to the process work directory, so they have to be provided as module inputs. By providing this file through...
Hello @alan-tracey, thanks for reporting this. I had a look at the `hCas9-TRAC` sample from the test data and in this case the masked bases are due to bad quality....
Could you check if the Ns are actually added by `seqtk`? You can find the output files after this tool in `preprocessing/seqtk`. By default we are using the parameter `-q...
Is the quality of those Ns higher than 20?
If you are using `--overrepresented`, the input reads to `seqtk` are under `/preprocessing/cutadapt`, could you doublecheck if the same reads which contain Ns after `seqtk`, also contain these Ns after...
Hi @dwreeves, thanks for all the information! I have tried your suggestion of adding a custom `CustomRichGroup` class and it works great. I think we can pin the version of...
Hi @dwreeves, thank you very much for this update! And sorry for not getting back to it. This will be very useful to simplify our code when the new version...
thanks for all the feedback! I am going to merge this PR then :)