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### Is your feature request related to a problem? Please describe
When using the cadd module, it has to download the environments used by the built-in snakemake pipeline every time the process is run…
fa2k updated
4 months ago
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Issue: Case F0059468 (cust002) have a pathogenic variant in KRT6B that was not called in the WGS analysis. We found out that our patient's sister with the same disease was analyzed in another laborato…
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[tomte](https://github.com/genomic-medicine-sweden/tomte) and other pipelines including [DROP](https://github.com/gagneurlab/drop) components will produce shortlists of aberrant expression (`OUTRIDER`…
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## Description
We now have three identical tests for the current nextflow pipelines, with unnecessary duplication.
## Suggested solution
We could refactor these to have one shared test. A ver…
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### 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 reason for bu…
fa2k updated
3 months ago
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From a slack conversation with @dnil it seems like the chromograph autozygosity tracks are missing.
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### Description of the bug
Sample names in `out/justhusky.tsv` are currently on the form `slowlycivilbuck_sorted_md` instead of `slowlycivilbuck`.
### Command used and terminal output
_No respons…
dnil updated
6 months ago
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### 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…
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### Is there an existing module for this?
- [X] I have searched for the existing module
### Is there an open PR for this?
- [X] I have searched for existing PRs
### Is there an open issue for this…
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https://github.com/nf-core/raredisease/blob/d18570a20270879c20102aae13269f08dc3ffb10/workflows/raredisease.nf#L163