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### Description of the bug
Hi,
I am running rnavar on a non-model organims species and I don't have vcf annotations or calibration for it. The pipeline runs after the mapping stage and it does not g…
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Hi!
I wanted to open a meta issue to consolidate all the efforts to actually get GATK4 to work (completely) through bioconda.
So far I've found draft PR's by
@mjsteinbaugh
@jmarshall
@ryanja…
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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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https://github.com/gatk-workflows
https://github.com/gatk-workflows/gatk4-rnaseq-germline-snps-indels
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### Is your feature request related to a problem? Please describe
- [x] bedtools/merge
- [x] bedtools/sort
- [x] cat/fastq
- [x] custom/dumpsoftwareversions
- [x] ensemblvep/vep
- [x] fastqc
- [x] ga…
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### Description of the bug
I get the below warning:
`WARN: A process with name 'GATK4_HAPLOTYPECALLERGVCF' is defined more than once in module script: /home/omeran/.nextflow/assets/nf-core/rnava…
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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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### Description of the bug
Dear All, I am facing a problem almost at the end of sarek version 3.1 for germline detection.
Could you please provide me assistance and help me to fix it?
Many Th…
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## Bug Report
### Affected tool(s)
_Tool name(s), special parameters?_
RenameSampleInVcf
### Affected version(s)
- [ ] Latest public release version [version?]
- [ ] Latest development/maste…
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Once GATK4.5.0.0 is out on DockerHub, we'll want to update it here