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FIX: misleading docs - xref 1621 #1623

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Aug 15, 2024
Merged

FIX: misleading docs - xref 1621 #1623

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534cf13
Update usage.md
maxulysse Aug 15, 2024
3e0c44c
Update CHANGELOG.md
maxulysse Aug 15, 2024
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4 changes: 3 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -9,12 +9,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Added

- [1614](https://github.com/nf-core/sarek/pull/1614) Back to dev
- [1614](https://github.com/nf-core/sarek/pull/1614) - Back to dev

### Changed

### Fixed

- [1623](https://github.com/nf-core/sarek/pull/1623) - Update docs to clarify vep cache folder organisation

### Removed

### Dependencies
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2 changes: 1 addition & 1 deletion docs/usage.md
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Expand Up @@ -871,7 +871,7 @@ To use these, supply the parameters `--vep_cache` and/or `--snpeff_cache` with t
### Specify the cache location

Params `--snpeff_cache` and `--vep_cache` are used to specify the locations to the root of the annotation cache folder.
The cache will be located within a subfolder with the path `${snpeff_species}.${snpeff_version}` for SnpEff and `${vep_species}/${vep_genome}_${vep_cache_version}` for VEP.
The cache will be located within a subfolder with the path `${snpeff_species}.${snpeff_version}` for SnpEff and `${vep_species}/${vep_cache_version}_${vep_genome}` for VEP.
If this directory is missing, Sarek will raise an error.

For example this is a typical folder structure for `GRCh38` and `WBCel235`, with SNPeff cache version 105 and VEP cache version 110:
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