From 534cf130c000172fd8a80714eac74ad38bf58533 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Thu, 15 Aug 2024 14:03:38 +0200 Subject: [PATCH 1/2] Update usage.md Fix #1621 --- docs/usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index 076cbfb04e..6a91830492 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -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: From 3e0c44c1323851a01723e825845ef7d14cd30994 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Thu, 15 Aug 2024 14:06:26 +0200 Subject: [PATCH 2/2] Update CHANGELOG.md --- CHANGELOG.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index bc027d6401..e786b51f10 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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