From 7c60096952539b7266cb82200f0dee77b5cef742 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Wed, 11 Mar 2020 14:17:24 +0100 Subject: [PATCH] update docs for munin/sarek specific config --- docs/pipeline/sarek/munin.md | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/docs/pipeline/sarek/munin.md b/docs/pipeline/sarek/munin.md index fc1636f..5f9511b 100644 --- a/docs/pipeline/sarek/munin.md +++ b/docs/pipeline/sarek/munin.md @@ -6,17 +6,22 @@ Extra specific configuration for sarek pipeline To use, run the pipeline with `-profile munin`. -This will download and launch the sarek specific [`munin.config`](../../../conf/pipeline/sarek/munin.config) which has been pre-configured with a setup suitable for the MUNIN cluster. +This will download and launch the sarek specific [`munin.config`](../../../conf/pipeline/sarek/munin.config) which has been pre-configured with a setup suitable for the `MUNIN` cluster. Example: `nextflow run nf-core/sarek -profile munin` ## Sarek specific configurations for MUNIN -Specific configurations for MUNIN has been made for sarek. +Specific configurations for `MUNIN` has been made for sarek. -* Params `annotation_cache` set to `true` -* Path to `snpEff_cache`: `/data1/cache/snpEff/` +* Params `annotation_cache` and `cadd_cache` set to `true` +* Params `vep_cache_version` set to `95` +* Path to `snpeff_cache`: `/data1/cache/snpEff/` * Path to `vep_cache`: `/data1/cache/VEP/` * Path to `pon`: `/data1/PON/vcfs/BTB.PON.vcf.gz` * Path to `pon_index`: `/data1/PON/vcfs/BTB.PON.vcf.gz.tbi` +* Path to `cadd_indels`: `/data1/cache/CADD/v1.4/InDels.tsv.gz` +* Path to `cadd_indels_tbi`: `/data1/cache/CADD/v1.4/InDels.tsv.gz.tbi` +* Path to `cadd_wg_snvs`: `/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz` +* Path to `cadd_wg_snvs_tbi`: `/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz.tbi` * Load module `Sentieon` for Processes with `sentieon` labels