Marius Bjørnstad
Marius Bjørnstad
We did the first half of this lesson as an online workshop today. The thing that caused the most problems was to start Jupyter Lab in the terminal / command...
The new Programming and Plotting with Python lesson uses Jupyter Lab. It would be good to mention Jupyter Lab in the installation instructions. (It's possible to have jupyter notebook installed,...
## Description of the bug I get a permission error when running the nf-core download command through Docker with the -u option to set the user & group IDs (as...
## Is your feature request related to a problem? Please describe The docker image doesn't contain singularity. I'd like to use the "download" command to download pipelines with singularity images....
### Description of feature Currently CADD has to create its internal conda environments, used in the snakemake pipeline, for each instance when a process is started. There are some good...
When running on some Debian-based Linux systems, it's not possible to run samtools 1.7. ``` samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file...
This PR solves a problem (#544 ), that not all alleles at a multiallelic indel site get a CADD score. The issue is that all indels aren't selected by `bcftools...
### Description of the bug Indels at positions with multiple alternative alleles end up without CADD scores (one of them get a CADD score). I've traced it to `ANNOTATE_SNVS:ANNOTATE_CADD:BCFTOOLS_VIEW`. The...
### Description of the bug I'm getting an error when trying to run the pipeline. The test profile works fine, so it's very likely that I'm doing something wrong, but...
### Is your feature request related to a problem? Please describe DeepVariant has three different stages, make_example, call_variants and postprocess_variants Currently all are being called from a single nextflow process,...