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**Is your feature request related to a problem in the current program to new available techology or software? Please describe and add links/citations if appropriate.**
It would be great to have acces…
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### Have you checked the docs?
- [X] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
- [X] [nf-core modules documentation](https://nf-co.re/docs/contributing/modules)
### …
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### Description of feature
Some of the annotation programs used in the pipeline only generate vcf outputs. It would be good to make changes to those modules so that they can also generate compressed …
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### Description of feature
Currently production uses a cg flag to rerun with bwa-mem 1.
Proposed implementation in raredisease: use the params config on servers to automatically change the container…
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**Describe the bug**
MT vars from `nf-core/raredisease` not displaying.
**To Reproduce**
Load split out MT VCFs
```scout load case -u scout_load.funkitten.yaml```
![Screenshot 2024-06-10 at …
dnil updated
3 months ago
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to align with output directories, config and possibly nf-core/raredisease (call_snv.nf)
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### Description of the bug
Get "bash: singularity: command not found" when running pipeline on slurm
### Command used and terminal output
```console
nextflow run nf-core/raredisease -r "patch" -pro…
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### Description of the bug
The crash:
```
ERROR ~ Cannot invoke method collectEntries() on null object
-- Check script './workflows/../subworkflows/nf-core/utils_nfcore_pipeline/main.nf' at…
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Hi!
I noticed that in our case 23289, the 3'UTR polymorphism c.*442_445delTAAA is visible in Scout, but not shown on the front page, although we have the variant saved as a managed variant. This is q…
MUebe updated
10 months ago
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Parsing VEP 110 files, especially as produced by the rarediesase pipe.
Attention to
- SO terms (do new terms mask old severe ones after "most severe" filtering)?
- Any changed annotation keys (IN…
dnil updated
2 months ago