From 709b9f045710442f09d47ba0e6e7bbd4404185ad Mon Sep 17 00:00:00 2001
From: SPearce <simon.pearce@cruk.manchester.ac.uk>
Date: Fri, 30 Jun 2023 10:39:21 +0100
Subject: [PATCH 1/2] Set queue based on memory

---
 conf/crukmi.config | 35 ++++++++++++++++++-----------------
 1 file changed, 18 insertions(+), 17 deletions(-)

diff --git a/conf/crukmi.config b/conf/crukmi.config
index b80343268..7d96746a2 100644
--- a/conf/crukmi.config
+++ b/conf/crukmi.config
@@ -1,54 +1,55 @@
 //Profile config names for nf-core/configs
 params {
   config_profile_description = 'Cancer Research UK Manchester Institute HPC cluster profile provided by nf-core/configs'
-  config_profile_contact = 'Stephen Kitcatt, Simon Pearce (@skitcattCRUKMI, @sppearce)'
-  config_profile_url = 'http://scicom.picr.man.ac.uk/projects/user-support/wiki'
+  config_profile_contact     = 'Stephen Kitcatt, Simon Pearce (@skitcattCRUKMI, @sppearce)'
+  config_profile_url         = 'http://scicom.picr.man.ac.uk/projects/user-support/wiki'
 }
 
 singularity {
-  cacheDir = '/lmod/nextflow_software'
-  enabled = true
+  cacheDir   = '/lmod/nextflow_software'
+  enabled    = true
   autoMounts = true
 }
 
 process {
-  beforeScript = 'module load apps/apptainer/1.0.0'
-  executor = 'slurm'
+  beforeScript = 'module load apps/apptainer/1.2.0'
+  executor     = 'slurm'
+  queue        = { task.memory <= 245.GB ? 'compute' : 'hmem' }
 
   errorStrategy = {task.exitStatus in [143,137,104,134,139,140] ? 'retry' : 'finish'}
-  maxErrors = '-1'
-  maxRetries = 3
+  maxErrors     = '-1'
+  maxRetries    = 3
 
   withLabel:process_single {
-    cpus = { check_max( 1 * task.attempt, 'cpus' ) }
+    cpus   = { check_max( 1 * task.attempt, 'cpus' ) }
     memory = { check_max( 5.GB * task.attempt, 'memory' ) }
   }
 
   withLabel:process_low {
-    cpus = { check_max( 1 * task.attempt, 'cpus' ) }
+    cpus   = { check_max( 1 * task.attempt, 'cpus' ) }
     memory = { check_max( 5.GB * task.attempt, 'memory' ) }
   }
 
   withLabel:process_medium {
-    cpus = { check_max( 4 * task.attempt, 'cpus' ) }
+    cpus   = { check_max( 4 * task.attempt, 'cpus' ) }
     memory = { check_max( 20.GB * task.attempt, 'memory' ) }
   }
 
   withLabel:process_high {
-    cpus = { check_max( 48 * task.attempt, 'cpus' ) }
-    memory = { check_max( 256.GB * task.attempt, 'memory' ) }
+    cpus   = { check_max( 48 * task.attempt, 'cpus' ) }
+    memory = { check_max( 240.GB * task.attempt, 'memory' ) }
   }
 
 }
 
 executor {
-    name = 'slurm'
-    queueSize = 1000
+    name         = 'slurm'
+    queueSize    = 1000
     pollInterval = '10 sec'
 }
 
 params {
   max_memory = 4000.GB
-  max_cpus = 96
-  max_time = 72.h
+  max_cpus   = 96
+  max_time   = 72.h
 }

From ff0fe6f32b81805b6244fa8be60e96c22a93b7bd Mon Sep 17 00:00:00 2001
From: SPearce <simon.pearce@cruk.manchester.ac.uk>
Date: Fri, 30 Jun 2023 10:40:57 +0100
Subject: [PATCH 2/2] Lower compute queue max to 240

---
 conf/crukmi.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/crukmi.config b/conf/crukmi.config
index 7d96746a2..7f5c2b74b 100644
--- a/conf/crukmi.config
+++ b/conf/crukmi.config
@@ -14,7 +14,7 @@ singularity {
 process {
   beforeScript = 'module load apps/apptainer/1.2.0'
   executor     = 'slurm'
-  queue        = { task.memory <= 245.GB ? 'compute' : 'hmem' }
+  queue        = { task.memory <= 240.GB ? 'compute' : 'hmem' }
 
   errorStrategy = {task.exitStatus in [143,137,104,134,139,140] ? 'retry' : 'finish'}
   maxErrors     = '-1'