Nicolas Vannieuwkerke comments

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                                            Nicolas Vannieuwkerke

AnnotSV BioConda Environment: Reference Issues For GRCh38

Strange :/ Can you give me some more information on your system? What OS are you using? What conda/mamba version are you using?

AnnotSV BioConda Environment: Reference Issues For GRCh38

Hmm all looks fine :/ It's very weird that you are getting these issues, I usually run the tool on a HPC too with singularity and have never encountered any...

AnnotSV BioConda Environment: Reference Issues For GRCh38

Then I'm not really sure this is something I can help you with :/ It doesn't seem like it's a singularity error, @lgmgeo could it be some bug in the...

ARRIBA_VISUALISATION depends on STAR-FUSIOn rather than ARRIBA ?

This has been fixed in the `dev` branch and will be available in the next release!

Error when working with `--ins-info-key`

Apparently the info field describing `SVINSSEQ` should look like this: ```txt ##INFO= ``` And the error happens when the header looks like this: ```txt ##INFO= ```

`nf-test` does not work with strict nextflow syntax.

This might get urgent pretty soon as the new syntax will probably become default at the end of October

Add comment about setting a default prefix that isn't just meta.id

Sorry for being difficult :grin: let's talk about it in the next meeting indeed :)

Failing to run on JDK 24

Same thing for Java 25, nf-test needs Java 11-18, bumping this is going to be necessary pretty soon since the newest Nextflow version supports Java 25

new module: vg/call

Awesome thank you! Can you create issues for all these new modules and add them to the project board? Maybe you'll get some help with them that way

Hi, please read the guidelines for this (https://nf-co.re/docs/contributing/modules#new-module-guidelines-and-pr-review-checklist) You'll find all answers there, but don't be afraid to ask me if something's not clear