Merge branch 'dev' into Sentieon

CHANGELOG.md

@@ -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]
 

docs/usage.md

@@ -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)
@@ -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.