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### Description of feature
As in raredisease config: https://github.com/nf-core/raredisease/blob/fec923acfb3ae183bbdfca7bbc1310371ab8b41d/nextflow.config
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### Description of the bug
ERROR ~ Error executing process > 'NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (13)'
Caused by:
Failed to pull singularity image
command:…
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### Description of the bug
Command output:
sbatch: s_p_parse_file: file "/cfs/klemming/home/h/halfdan/.atp/x86_64/slurm.conf" is empty
sbatch: error: ClusterName needs to be specified
sbatch…
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## Description
We've been incorrectly populating the `started_at` field in Statusdb. This field is supposed to be derived from the creation date of the `_deliverables.yaml` file. For MIP, the deliv…
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There is a mtDNA deletion in case 23103, which is not called in Scout. We have confirmed it with MLPA and also sequenced the breakpoints by sanger sequencing. I recently found mtDNA deletions in two o…
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**Describe the bug**
Our geneticists asked whether the compound top 20 on the SNV/indel page works as intended.
Here is one example:
![compound_page](https://github.com/user-attachments/asset…
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- [ ] MT variants VCF
~MT variants rank model key~
~MT variants rank model file (link on e.g. reference-files)~
We keep the same variant type (SNV on the chromosome MT).
We postpone making a ne…
dnil updated
3 months ago
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### Description of the bug
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /cfs/klemming/home/h/halfdan/nfc_rd/test_full/work/singularity -- Use the…
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To be invoked by cg to create the delivery report, see https://github.com/Clinical-Genomics/cg/pull/3267
Should ideally accept a query like this:
```
query = {
"build" : "GRCh37"
"sam…
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### Description of the bug
The vcfs from tomte are not compatible with scout. Scout requires only one alternative per line
This can be fixed by:
```
bcftools norm -m -both input.vcf.gz > outpu…