From f793ffaace6d86460f2b515912d958f1c293b77b Mon Sep 17 00:00:00 2001 From: Rogan Grant Date: Tue, 3 Aug 2021 15:10:54 -0500 Subject: [PATCH] Updated iGenomes location --- conf/nu_genomics.config | 2 +- docs/nu_genomics.md | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/conf/nu_genomics.config b/conf/nu_genomics.config index 690c22e..3598a31 100644 --- a/conf/nu_genomics.config +++ b/conf/nu_genomics.config @@ -7,7 +7,7 @@ params max_memory = 190.GB max_cpus = 40 max_time = 240.h - igenomes_base = "/projects/genomicsshare/igenomes" + igenomes_base = "/projects/genomicsshare/AWS_iGenomes" } singularity diff --git a/docs/nu_genomics.md b/docs/nu_genomics.md index 4c2034f..21fc2b4 100644 --- a/docs/nu_genomics.md +++ b/docs/nu_genomics.md @@ -32,5 +32,4 @@ module load graphviz/2.40.1 ## Use of iGenomes -A local copy of the iGenomes resource with all commonly used genomes has been made available for all of Quest so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. -You can do this by simply using the `--genome ` parameter. While you can technically "stream" genomes from iGenomes directly using the pipeline, this is a substantial use of bandwidth and resources on both ends, and potentially poses reproducibility issues later on. Please use the local copies unless absolutely necessary, and save your custom genomes to your personal allocation where necessary. +A local copy of the iGenomes resource with all commonly used genomes has been made available for all of Quest so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. These files can be found at `/projects/genomicsshare/AWS_iGenomes`. You can do this by simply using the `--genome ` parameter. While you can technically "stream" genomes from iGenomes directly using the pipeline, this is a substantial use of bandwidth and resources on both ends, and potentially poses reproducibility issues later on. Please use the local copies unless absolutely necessary, and save your custom genomes to your personal allocation where necessary.