Marius Bjørnstad

After some discussion, we decided to try to make a longer set of setup instructions that includes opening the notebook and checking that the data folder is there. This will...

Yes it works perfectly for the rnaseq pipeline. Downloads all the images. Maybe it's not that common, but our system is completely offline. I was hoping to transfer the pipeline...

I'm sorry to comment on this old fixed issue, but I had the exact same problem, and it was solved by following the procedure here. It's quite hard to find...

> What is the use case? I work with patient data, and due to confidentiality and IT security requirements, the sequence data are currently held in an "air-gapped" infrastructure -...

Thanks a lot for this @MariaNattestad , fantastic!

The test profile works perfectly for this `patch` branch on RHEL 9 and Fedora 39 with singularity and local executor (no executor/cluster setting). [I am testing 2.0.1 with a full-scale...

I've made a draft version of this. This is just to have something concrete to look at - I don't think it's necessarily the right way, as I don't know...

I've made it run with both the existing test and a new test for bam input (and cleaned up a bit). The test outputs are not identical, but I've checked...

I have updated to integrate the upstream changes from `dev`. Will make a pull request.

> Any updates on this feature? Starting from bam-files would be extremely useful. Sorry for the late reply. As far as I know, there is no work that has been...