From 38a05a6531051067a4c97e2fa8561899cfdf61fd Mon Sep 17 00:00:00 2001
From: Combiz Khozoie <31043044+combiz@users.noreply.github.com>
Date: Thu, 10 Feb 2022 23:46:14 +0000
Subject: [PATCH] Update imperial.config

Reworked to use internal profiles for the Imperial HPC and the MedBio cluster.
---
 conf/imperial.config | 114 ++++++++++++++++++++++++++-----------------
 1 file changed, 70 insertions(+), 44 deletions(-)

diff --git a/conf/imperial.config b/conf/imperial.config
index e2a3aca..26742f2 100644
--- a/conf/imperial.config
+++ b/conf/imperial.config
@@ -1,14 +1,76 @@
 //Profile config names for nf-core/configs
 
-params {
-    // Config Params
-    config_profile_description = 'Imperial College London - HPC Profile -- provided by nf-core/configs.'
-    config_profile_url = 'https://www.imperial.ac.uk/admin-services/ict/self-service/research-support/rcs/'
+profiles {
+    imperial {
+        params {
+            // Config Params
+            config_profile_description = 'Imperial College London - HPC Profile -- provided by nf-core/configs.'
+            config_profile_contact = 'Combiz Khozoie (c.khozoie@imperial.ac.uk)'
+            config_profile_url = 'https://www.imperial.ac.uk/admin-services/ict/self-service/research-support/rcs/'
 
-    // Resources
-    max_memory = 480.GB
-    max_cpus = 40
-    max_time = 1000.h
+            // Resources
+            max_memory = 480.GB
+            max_cpus = 40
+            max_time = 1000.h
+        }
+
+        process {
+            executor = 'pbspro'
+
+            // Process-specific resource requirements
+            withLabel:process_low {
+                // TARGET QUEUE: throughput
+                cpus   = { 2     * task.attempt }
+                memory = { 12.GB * task.attempt }
+                time   = { 4.h   * task.attempt }
+            }
+            withLabel:process_medium {
+                // TARGET QUEUE: throughput
+                cpus   = 8
+                memory = { 32.GB * task.attempt }
+                time   = { 8.h   * task.attempt }
+            }
+            withLabel:process_high {
+                // TARGET QUEUE: general
+                cpus   = 32
+                memory = { 62.GB * task.attempt }
+                time   = { 16.h  * task.attempt }
+            }
+            withLabel:process_long {
+                // TARGET QUEUE: long
+                cpus   = 8
+                memory = 96.GB
+                time   = { 72.h  * task.attempt }
+            }
+            withLabel:process_high_memory {
+                // TARGET QUEUE: large memory
+                cpus   = { 10     * task.attempt }
+                memory = { 120.GB * task.attempt }
+                time   = { 12.h   * task.attempt }
+            }
+        }
+    }
+    medbio {
+        params {
+            // Config Params
+            config_profile_description = 'Imperial College London - MEDBIO QUEUE - HPC Profile -- provided by nf-core/configs.'
+            config_profile_contact = 'Combiz Khozoie (c.khozoie@imperial.ac.uk)'
+            config_profile_url = 'https://www.imperial.ac.uk/bioinformatics-data-science-group/resources/uk-med-bio/'
+
+            // Resources
+            max_memory = 480.GB
+            max_cpus = 40
+            max_time = 1000.h
+        }
+
+        process {
+            executor = 'pbspro'
+
+            queue = 'pqmedbio-tput'
+
+        //queue = 'med-bio' //!! this is an alias and shouldn't be used
+        }
+    }
 }
 
 executor {
@@ -28,39 +90,3 @@ singularity {
     autoMounts = true
     runOptions = "-B /rds/,/rds/general/user/$USER/ephemeral/tmp/:/tmp,/rds/general/user/$USER/ephemeral/tmp/:/var/tmp"
 }
-
-process {
-    executor = 'pbspro'
-
-    // Process-specific resource requirements
-    withLabel:process_low {
-        // TARGET QUEUE: throughput
-        cpus   = { check_max( 2     * task.attempt,  'cpus'   ) }
-        memory = { check_max( 12.GB * task.attempt,  'memory' ) }
-        time   = { check_max( 4.h   * task.attempt,  'time'   ) }
-    }
-    withLabel:process_medium {
-        // TARGET QUEUE: throughput
-        cpus   = { check_max( 8,                     'cpus'   ) }
-        memory = { check_max( 32.GB * task.attempt,  'memory' ) }
-        time   = { check_max( 8.h   * task.attempt,  'time'   ) }
-    }
-    withLabel:process_high {
-        // TARGET QUEUE: general
-        cpus   = { check_max( 32,                    'cpus'   ) }
-        memory = { check_max( 62.GB * task.attempt,  'memory' ) }
-        time   = { check_max( 16.h  * task.attempt,  'time'   ) }
-    }
-    withLabel:process_long {
-        // TARGET QUEUE: long
-        cpus   = { check_max( 8,                     'cpus'   ) }
-        memory = { check_max( 96.GB,                 'memory' ) }
-        time   = { check_max( 72.h  * task.attempt,  'time'   ) }
-    }
-    withLabel:process_high_memory {
-        // TARGET QUEUE: large memory
-        cpus   = { check_max( 10     * task.attempt, 'cpus'   ) }
-        memory = { check_max( 120.GB * task.attempt, 'memory' ) }
-        time   = { check_max( 12.h   * task.attempt, 'time'   ) }
-    }
-}