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Want to run this command from within Biokepi pipelines (to merge multiple VCFs):
```
varlens-variants
--variants MOSAIK_Mutect.vcf
--variants MOSAIK_Strelka.vcf
--variants BWA_Mutect.vcf
--varian…
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### Description of feature
https://www.zymoresearch.de/products/zymo-seq-switchfree-3-mrna-library-kit
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I'm trying to get this running on Google Cloud Platform using [https://github.com/broadinstitute/wdl-runner](url)
Unfortunately, the outputDir is pervasive throughout the WDL files and seems to be a …
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Copying @vsatheesh's message from slack and https://github.com/isugifNF/GATK-flow/pull/16#issuecomment-2231427609 to a separate Issue, since this is unrelated to the SNPeff PR.
> After adding thes…
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In order to simplify the handling of data throughout the pipeline, it would be good to normalize the format of the data as much as possible, starting with the raw data sources.
Currently we have:
**…
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### Description of the bug
Hi
I tried to skip all preprocessing qc steps using the following skipping options but I got a java null error on some path value:
**nf-params.json**:
```json
{
…
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### Description of feature
When analyzing a large number of samples using the differential abundance pipeline, the markdown notebook compilation step fails due to memory issues.
- Error message: "…
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Hi there,
I'd like to try using circompara2 to map circRNA reads in human genome for my RNAseq project. But since my project has over 1000 samples and we've already done the alignment work for mRNA b…
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Add proper documentation to explain how to properly use it and implement it in the pipelines
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Add benchmarking to every rule
Also write the time to run it all to a log?
[PR-29]
[PR-29]: https://clinicalgenomics.atlassian.net/browse/PR-29
ghost updated
3 years ago