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### Description of feature
The deepvariant process could be split into 3 parts and made into a workflow. This would better allocate resources, mainly since the last step is single/threaded and takes …
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Hello developers,
MARRVEL has released a new tool called MARRVELAI. This tool integrates phenotype data to prioritize variants, a feature currently missing in Scout's variant ranking. MARRVELAI can…
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**Is your feature request related to a problem? Please describe.**
It would be nice if we can move [this](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/docs/usage.md#azure-re…
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### Description of the bug
```
$ nf-core subworkflows test --profile docker
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ …
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Please convert each of this as an issue when you start working on one.
(That can be done by clicking on the circle dot `⊙` at the end of the line in the list below, hover on a list item to see it)
A…
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Current samplesheets for raredisease look like below. As you can see, the lane field indicates the lane number where the sample was run in the flowcell.
```
sample,lane,fastq_1,fastq_2,sex,phenot…
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**Describe the bug**
The Raredisease workflow is not storing the d4 coverage file necessary for reporting coverage in the delivery report.
As per the implementation in [Clinical-Genomics/cg#3459…
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I think it would be good to have a module for [gatk4](https://bioconda.github.io/recipes/gatk4/README.html)
Needed for integrating [Gens](https://github.com/Clinical-Genomics-Lund/gens) into the …
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### Description of feature
It would be nice to have entry points for different parts of the pipeline ex. snv/sv annotation, mitochondrial analysis.
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Hello
I found a variant that consist of two nucleotides on the same allele (reads) that was only called as single nucleotide change (times two). Whats your thinking?
https://scout.scilifelab.se/ig…