Anders Sune Pedersen

https://nfcore.slack.com/channels/sarek

What error are you getting? Can you paste the error message here? Did you set the nextflow secret for sentieon? Sarek v3.4 runs Sentieon:202112.06. However, the version of Sarek on...

Turns out the new `.bundle`-format was introduced as part of Sentieon 202308. Sarek v3.4 uses an earlier version of Sentieon, that is, 202112.06. Now, the current dev-version of Sarek implements...

That is a bug :-/ Thanks for uncovering this. It is due to the fact that your command uses Apptainer. We got a similar error with Singularity, and so we...

@maxulysse :The bug related to apptainer is an easy fix (as I'm sure you'll agree), but we need to fix it in the modules-repo. AFAIK, the CI-tests don't run apptainer,...

I don't suppose the CI-tests of Sentieon will pass: https://github.com/nf-core/modules/pull/4893

I ran the pytests for Sentieon locally with singularity: ``` TMPDIR=/ngc/projects/bio/people/andped/tmp PROFILE=singularity pytest --tag sentieon --symlink --kwdof --color=yes ... === 270 passed, 1424 skipped, 1 warning in 1303.74s (0:21:43) ===...

> Hi, > > I updated to tehn latest dev version and it seems ok now. > > I am assuming I should not use the "--sentieon_dnascope_model" option as this...

I also reported that error: https://github.com/nf-core/sarek/issues/1146 Could you try running the pipeline with the option `--skip_tools haplotyper_filter`? https://nf-co.re/sarek/3.4.0/parameters#skip_tools

Come on over on nf-core/sarek slack, and let's take a look at those errors