From bdf4a829b808ec601ebc456669f6a707c5908e6d Mon Sep 17 00:00:00 2001
From: phue <patrick.huether@gmail.com>
Date: Tue, 26 Nov 2019 14:22:16 +0100
Subject: [PATCH 1/2] roll out iGenomes on cbe

---
 conf/cbe.config | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/conf/cbe.config b/conf/cbe.config
index 6e47361..3332b1e 100755
--- a/conf/cbe.config
+++ b/conf/cbe.config
@@ -12,12 +12,14 @@ process {
   clusterOptions = { task.time <= 8.h ? '--qos short': task.time <= 48.h ? '--qos medium' : '--qos long' }
 }
 
-singularity.enabled = true
+singularity {
+  enabled = true
+  cacheDir = '/scratch-cbe/shared/containers'
+}
 
 params {
   params.max_time = 14.d
   params.max_cpus = 36
   params.max_memory = 4.TB
-  igenomes_ignore = true
-  igenomesIgnore = true //deprecated
-}
\ No newline at end of file
+  igenomes_base = '/resources/references/igenomes'
+}

From 672f025639ca52a95dce9aee8a23c1bc52f2bad2 Mon Sep 17 00:00:00 2001
From: phue <patrick.huether@gmail.com>
Date: Tue, 26 Nov 2019 18:09:20 +0100
Subject: [PATCH 2/2] cbe: add documentation about iGenomes

---
 docs/cbe.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/docs/cbe.md b/docs/cbe.md
index 5b17a15..8d597a0 100644
--- a/docs/cbe.md
+++ b/docs/cbe.md
@@ -13,5 +13,7 @@ module load nextflow/19.04.0
 module load singularity/3.2.1
 ```
 
+A local copy of the [AWS-iGenomes](https://registry.opendata.aws/aws-igenomes/) resource has been made available on CBE 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 <GENOME_ID>` parameter.
+
 >NB: You will need an account to use the HPC cluster on CBE in order to run the pipeline. If in doubt contact IT.
 >NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT.