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Update docs #194

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4 changes: 2 additions & 2 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -53,10 +53,10 @@ Piellorieppe is one of the main massif in the Sarek National Park.
- [#141](https://github.com/nf-core/sarek/pull/141) - Update `VEP` databases to `99`
- [#143](https://github.com/nf-core/sarek/pull/143) - Revert `snpEff` cache version to `75` for `GRCh37`
- [#143](https://github.com/nf-core/sarek/pull/143) - Revert `snpEff` cache version to `86` for `GRCh38`
- [#152](https://github.com/nf-core/sarek/pull/152), [#158](https://github.com/nf-core/sarek/pull/158), [#164](https://github.com/nf-core/sarek/pull/164), [#174](https://github.com/nf-core/sarek/pull/174) - Update docs
- [#152](https://github.com/nf-core/sarek/pull/152), [#158](https://github.com/nf-core/sarek/pull/158), [#164](https://github.com/nf-core/sarek/pull/164), [#174](https://github.com/nf-core/sarek/pull/174), [#194](https://github.com/nf-core/sarek/pull/194) - Update docs
- [#164](https://github.com/nf-core/sarek/pull/164) - Update `gatk4-spark` from `4.1.4.1` to `4.1.6.0`
- [#180](https://github.com/nf-core/sarek/pull/180) - Improve minimal setting
- [#183](https://github.com/nf-core/sarek/pull/183) - Update input.md documentation
- [#183](https://github.com/nf-core/sarek/pull/183) - Update `input.md` documentation

### Fixed - [2.6dev]

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28 changes: 28 additions & 0 deletions docs/usage.md
Original file line number Diff line number Diff line change
Expand Up @@ -74,6 +74,9 @@
- [--species](#--species)
- [--vep_cache_version](#--vep_cache_version)
- [--vepCacheVersion](#--vepcacheversion)
- [--annotation_cache](#--annotation_cache)
- [--snpeff_cache](#--snpeff_cache)
- [--vep_cache](#--vep_cache)
- [--igenomes_ignore](#--igenomes_ignore)
- [--igenomesIgnore](#--igenomesignore)
- [Job resources](#job-resources)
Expand Down Expand Up @@ -752,6 +755,31 @@ If you prefer, you can specify the cache version when you run the pipeline:
> :warning: This params has been removed.
> Please check: [`--vep_cache_version`](#--vep_cache_version)

### --annotation_cache

Enable usage of annotation cache, and disable usage of already built containers within Sarek.
For more information, follow the [annotation guidelines](annotation.md#using-downloaded-cache).

```bash
--annotation_cache
```

### --snpeff_cache

To be used conjointly with [`--annotation_cache`](#--annotation_cache), specify the cache snpEff directory:

```bash
--snpeff_cache /path/to/snpeff_cache
```

### --vep_cache

To be used conjointly with [`--annotation_cache`](#--annotation_cache), specify the cache VEP directory:

```bash
--vep_cache /path/to/vep_cache
```

### --igenomes_ignore

Do not load `igenomes.config` when running the pipeline.
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