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See: https://github.com/fulcrumgenomics/fgbio
> A set of tools to analyze genomic data with a focus on Next Generation Sequencing.
Currently available in the toolshed:
- [FastqToBam](https://…
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### Have you checked the docs?
- [X] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
- [X] [nf-core modules documentation](https://nf-co.re/docs/contributing/modules)
### …
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`fgbio` PRs are expected to adhere to "tim-format," which encompasses Nils and Tim's preferred conventions for formatting Scala code.
e.g. https://github.com/fulcrumgenomics/fgbio/pull/958#discussi…
msto updated
2 months ago
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Some tools that work with extracted UMIs expect a specific delimiter between umi1 and umi2 (assuming each read has its own UMI). E.g. fgbio CopyUmiFromReadName (https://fulcrumgenomics.github.io/fgbio…
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**Version info**
- bcbio version (`bcbio_nextgen.py --version`): 1.2.9
- OS name and version (`lsb_release -ds`): "CentOS Linux release 7.9.2009 (Core)"
- Manta: 1.6.0
- fgbio: 1.4.0
**To Repro…
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Consider using the automated tool to facilitate this https://nf-co.re/docs/contributing/modules#migrating-from-pytest-to-nf-test
### Is your feature request related to a problem? Please describe
…
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Hello,
To get my reads into the originalName#UMI format in a bam file, I am running:
1) picard FastqToSam
2) fgbio ExtractUMIsFromBam (get reads in originalName#UMI format)
3) picard SamToFas…
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hello! I'm doing with sequencing data with UMI, I followed [#fgbio-best-practise-fastq---consensus-pipeline](https://github.com/fulcrumgenomics/fgbio/blob/3a74fd28ff630b417410953541ff107a1b7b0fb7/docs…
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Dear all,
I've been trying to use `fgbio CorrectUmis` to process some data from Illumina's TSO500, but they use a mixture of 6bp and 7bp UMIs.
Since `bcl2fastq` needs a fixed length UMI, we've…
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### Description of feature
See: https://github.com/nf-core/fastquorum/pull/42#discussion_r1608511337
E.g. add metrics produced by `GroupReadsByUmi`: See: https://github.com/MultiQC/MultiQC/blob/ma…
nh13 updated
3 months ago