From 79899c3966ad6120f8cf0ed976a7c9f0c9407bf0 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Wed, 25 Sep 2024 12:43:31 +0200
Subject: [PATCH] Remove unused check_max() functions from configs

---
 conf/rosalind_uge.config | 50 ++++++++--------------------------------
 conf/uge.config          | 46 ++++++------------------------------
 2 files changed, 16 insertions(+), 80 deletions(-)

diff --git a/conf/rosalind_uge.config b/conf/rosalind_uge.config
index 6f5a1a019..20369bde3 100644
--- a/conf/rosalind_uge.config
+++ b/conf/rosalind_uge.config
@@ -8,62 +8,30 @@
 // Basic params of config file
 params {
     config_profile_description = 'Rosalind UGE config file'
-    config_profile_contact = 'Gregory Sprenger (@gregorysprenger)'
+    config_profile_contact     = 'Gregory Sprenger (@gregorysprenger)'
 }
 
 // Use Singularity
 singularity {
-    enabled = true
+    enabled    = true
     autoMounts = true
 }
 
 // Submit up to 100 jobs at once with 15 secs between to avoid spamming the cluster
 executor {
-    queueSize = 100
+    queueSize    = 100
     pollInterval = '15 sec'
 }
 
 // Process specific resource requirements
 process {
     // Error and retry handling
-    errorStrategy = { task.exitStatus in [143,137,104,134,139,71,255] ? 'retry' : 'finish' }
-    maxRetries    = 3
+    errorStrategy  = { task.exitStatus in [143, 137, 104, 134, 139, 71, 255] ? 'retry' : 'finish' }
+    maxRetries     = 3
 
     // Executor and queue information
-    executor = 'sge'
-    penv = 'smp'
-    queue = { task.time <= 4.h ? 'short.q' : task.time > 5.h ? 'all.q' : 'short.q' }
-    clusterOptions = { "-l h_vmem=${task.memory.toString().replaceAll(/[\sB]/,'')}" }
-}
-
-// Function to ensure that resource requirements don't go beyond limit
-def check_max(obj, type) {
-    if (type == 'memory') {
-        try {
-            if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
-                return params.max_memory as nextflow.util.MemoryUnit
-            else
-                return obj
-        } catch (all) {
-            println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
-            return obj
-        }
-    } else if (type == 'time') {
-        try {
-            if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
-                return params.max_time as nextflow.util.Duration
-            else
-                return obj
-        } catch (all) {
-            println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
-            return obj
-        }
-    } else if (type == 'cpus') {
-        try {
-            return Math.min( obj, params.max_cpus as int )
-        } catch (all) {
-            println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
-            return obj
-        }
-    }
+    executor       = 'sge'
+    penv           = 'smp'
+    queue          = { task.time <= 4.h ? 'short.q' : task.time > 5.h ? 'all.q' : 'short.q' }
+    clusterOptions = { "-l h_vmem=${task.memory.toString().replaceAll(/[\sB]/, '')}" }
 }
diff --git a/conf/uge.config b/conf/uge.config
index 2b82da42a..53e998f0e 100644
--- a/conf/uge.config
+++ b/conf/uge.config
@@ -8,61 +8,29 @@
 // Basic params of config file
 params {
     config_profile_description = 'Univa Grid Engine config file'
-    config_profile_contact = 'Gregory Sprenger (@gregorysprenger)'
+    config_profile_contact     = 'Gregory Sprenger (@gregorysprenger)'
 }
 
 // Use Singularity
 singularity {
-    enabled = true
+    enabled    = true
     autoMounts = true
 }
 
 // Submit up to 100 jobs at once with 15 secs between to avoid spamming the cluster
 executor {
-    queueSize = 100
+    queueSize    = 100
     pollInterval = '15 sec'
 }
 
 // Process specific resource requirements
 process {
     // Error and retry handling
-    errorStrategy = { task.exitStatus in [143,137,104,134,139,71,255] ? 'retry' : 'finish' }
+    errorStrategy = { task.exitStatus in [143, 137, 104, 134, 139, 71, 255] ? 'retry' : 'finish' }
     maxRetries    = 3
 
     // Executor and queue information
-    executor = 'sge'
-    penv = 'smp'
-    queue = { task.time <= 4.h ? 'short.q' : task.time > 5.h ? 'all.q' : 'short.q' }
-}
-
-// Function to ensure that resource requirements don't go beyond limit
-def check_max(obj, type) {
-    if (type == 'memory') {
-        try {
-            if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
-                return params.max_memory as nextflow.util.MemoryUnit
-            else
-                return obj
-        } catch (all) {
-            println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
-            return obj
-        }
-    } else if (type == 'time') {
-        try {
-            if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
-                return params.max_time as nextflow.util.Duration
-            else
-                return obj
-        } catch (all) {
-            println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
-            return obj
-        }
-    } else if (type == 'cpus') {
-        try {
-            return Math.min( obj, params.max_cpus as int )
-        } catch (all) {
-            println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
-            return obj
-        }
-    }
+    executor      = 'sge'
+    penv          = 'smp'
+    queue         = { task.time <= 4.h ? 'short.q' : task.time > 5.h ? 'all.q' : 'short.q' }
 }