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I'm getting the following error loading a case from nf-raredisease into a fresh install of Scout:
```
Traceback (most recent call last):
File "/home/fearnleyl/scout/scout/adapter/mongo/variant…
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Lims Issue
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For definitions of headings below see [Basic Concepts](https://atlas.scilifelab.se/infrastructure/lims/basic_concepts/).
**Work Flow:** Full name here please!
**Prot…
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Possible alternatives are not compatible with the ones in the documentation.(PED file format: Sex (1=male; 2=female; other=unknown))
https://github.com/nf-core/raredisease/blob/1489b71cc0e15ade7e9…
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### 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 I can't figure it out. I have not…
fa2k updated
3 months ago
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### Description of the bug
See https://github.com/Clinical-Genomics/scout/issues/4397 and https://github.com/Clinical-Genomics/scout/pull/4577. In particular we identify the DOMAINS field of the INFO…
dnil updated
3 months ago
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As a clinician or researcher, I want SNVs to be annotated, ranked and compatible with Scout.
# Suggested approach
Multisample/case_id vcfs are annotated, then split after annotation.
#### Annotate …
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### Description of the bug
When launching the raredisease pipeline using cg workflow raredisease run CASE, the job terminates in nf-tower with the following error:
```
`N E X T F L O W ~ version 2…
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### Description of feature
https://github.com/PacificBiosciences/paraphase
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call_sv_germlinecnvcaller.nf use GATK4_GERMLINECNVCALLER.out.calls
https://github.com/nf-core/raredisease/blob/752a9e172d710c8c67bbb6791955c91eb6f5fbde/subworkflows/local/variant_calling/call_sv_germ…
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We already do
```
peddy_check: /home/proj/stage/rare-disease/raredisease_output_justhusky_cache110/peddy_check/justhusky.ped_check.csv
peddy_ped: /home/proj/stage/rare-disease/raredisease_output_ju…
dnil updated
6 months ago