diff --git a/CHANGELOG.md b/CHANGELOG.md index 240f729805..bb6d2b89e9 100644 --- a/CHANGELOG.md +++ b/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] diff --git a/docs/usage.md b/docs/usage.md index 8ff9cb793a..d3787f7f3b 100644 --- a/docs/usage.md +++ b/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.