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- Add new workflow and protocol to WF chain
- File should be a TSV
Automate sample sheet for Feiyu so that he knows which samples of ours are in a sequencing run
- Need Runsheet for sequencer
- Samp…
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Check if all plugin examples are still working and up to date. Add some extra comments if needed?
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### Description of the bug
Good evening,
I am experiencing problems with Sarek's pipeline. When I try to remove the adapters from my WES data, the dragmap tool runs into "Segmentation Fault".
Do y…
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https://github.com/nf-core/sarek/pull/1358
```console
.command.sh: line 8: 36 Segmentation fault (core dumped) dragen-os -r narfmap --RGSM test_test --RGID "@RG\tID:null.test.test_L1\tPU:t…
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Hi,
I want to test dragmap (currently I'm using Bwa mem2) but I get an error.
First precision : I use dragmap with a Conda env, the last version.
Command used:
```
dragen-os \
-r ${REF_Gen…
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### Description of the bug
[my_param.json](https://github.com/user-attachments/files/15766958/my_param.json)
> > error [nextflow.exception.ProcessFailedException]: Process `NFCORE_SAREK:SAREK:F…
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## Bug Report
### Affected tool(s) or class(es)
GnarlyGenotyper
### Affected version(s)
- [ ] Latest public release version [version?]
- [ ] Latest master branch as of [date of test?]
- [x] …
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### Need
MSI analysis was requested to be included to the workflow in https://github.com/Clinical-Genomics/BALSAMIC/issues/972
### Suggested approach
Add [MSIsensor-pro](https://github.com/x…
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My command:
`dotnet.exe .\Downloader.dll --ga GRCh38 -o D:\NirvanaDB_2\`
Version of downloader: 3.18.1-0-g05f88047
I always get `truncated` for the same three dbs:
```
DANN_20200205.gsa (GR…
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Hi! I am using samtools 1.6. I tried to use global option reference with command, index. But it doesn't seem like samtools recognizes this option.
Manual that I used: http://www.htslib.org/doc/sa…