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### Description of the bug
I've run into an issue running the Sarek pipeline with Sea Urchin genome data. I would like to run Manta to find all variants from short read DNA sequencing data. I have al…
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Greetings,
I have a paired somatic pipeline and two of the callers it uses are vardict and varscan2, which will output germline calls as well. I wanted to include them into my VLR candidates beca…
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We need to review what https://nf-co.re/sarek can do to determine:
- if it could be used as is
- if it could be used with modifications
- if we'd rather extract and replicate some functionality h…
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### Description of feature
We are currently using a minimal test dataset for SARS-CoV-2 which is sufficient to test the pipeline but we don't have dbSNP and indel files for this reference.
It woul…
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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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This subworkflow will cover the gatk4 best practices workflow: https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels- starting with the analys…
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**Is your feature request related to a problem? Please describe.**
We need to create a minimal germline variant calling pipeline use case setup here
- https://github.com/bihealth/snappy-use-case-g…
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I got this error when I run the following commands;
```
singularity pull clairs.sif docker://hkubal/clairs:latest
singularity exec --bind /truba/home/erdikilic/pacbio_nd_t:/data clairs.sif /opt/b…
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Hi
thanks for putting together these great learning resources.
Would it be possible to add the correct answers and some explanations to the exercises at the end of [intro lesson 00](https://gith…
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### Description of the bug
As title states, we used to have it but apparently not anymore, see here: https://nfcore.slack.com/archives/CGFUX04HZ/p1697021363120009
### Command used and terminal outpu…