From 58508c4fbc27bd71c82a16f6ec2bee277bc53aea Mon Sep 17 00:00:00 2001
From: Priyanka Surana <ps22@sanger.ac.uk>
Date: Wed, 20 Jul 2022 13:14:42 +0100
Subject: [PATCH] Sanger profile update

---
 conf/sanger.config | 46 ++++++++++++++++++++++------------------------
 1 file changed, 22 insertions(+), 24 deletions(-)

diff --git a/conf/sanger.config b/conf/sanger.config
index 1955ca9..df2dee7 100644
--- a/conf/sanger.config
+++ b/conf/sanger.config
@@ -1,35 +1,33 @@
+// Profile details
 params {
-  config_profile_description = 'The Wellcome Sanger Institute HPC cluster profile'
-  config_profile_contact = 'Anthony Underwood (@aunderwo)'
-  config_profile_url = 'https://www.sanger.ac.uk/group/informatics-support-group/'
-}
-
-singularity {
-  enabled = true
-  cacheDir   = "${baseDir}/singularity"
-  runOptions = '--bind /lustre --bind /nfs/pathnfs01 --bind /nfs/pathnfs02 --bind /nfs/pathnfs03 --bind /nfs/pathnfs04 --bind /nfs/pathnfs05 --bind /nfs/pathnfs06 --no-home'
+    config_profile_description = 'The Wellcome Sanger Institute HPC cluster (farm5) profile'
+    config_profile_contact = 'Priyanka Surana (@priyanka-surana)'
+    config_profile_url = 'https://www.sanger.ac.uk'
 }
 
+// Queue and retry strategy
 process{
-  executor = 'lsf'
-  queue = 'normal'
-  errorStrategy = { task.attempt <= 5 ? "retry" : "finish" }
-  process.maxRetries = 5
-  withLabel:process_long {
-    queue = 'long'
-  }
+    executor = 'lsf'
+    queue = { task.time < 12.h ? 'normal' : task.time < 48.h ? 'long' : 'basement' }
+    errorStrategy = 'retry'
+    maxRetries = 5
 }
 
+// Executor details
 executor{
-  name = 'lsf'
-  perJobMemLimit = true
-  poolSize = 4
-  submitRateLimit = '5 sec'
-  killBatchSize = 50
+    name = 'lsf'
+    perJobMemLimit = true
+    poolSize = 4
+    submitRateLimit = '5 sec'
+    killBatchSize = 50
 }
 
+// Max resources
 params {
-  max_memory = 128.GB
-  max_cpus = 64
-  max_time = 48.h
+    max_memory = 683.GB
+    max_cpus = 256
+    max_time = 720.h
 }
+
+// For singularity
+singularity.runOptions = '--bind /lustre --bind /nfs'