diff --git a/conf/incliva.config b/conf/incliva.config
index 6c2a85a5a..0a0912af3 100644
--- a/conf/incliva.config
+++ b/conf/incliva.config
@@ -3,6 +3,13 @@ params {
     config_profile_description = 'INCLIVA Health Research Institute profile for nf-core.'
     config_profile_contact = 'Sheila Zúñiga Trejos - bioinfo@incliva.es'
     config_profile_url = 'https://www.incliva.es/en/services/platforms/bioinformatics-unit/'
+    hostname = 'hostname'.execute().text.trim() ?: 'unknown'
+    max_memory = params.hostname == 'vlinuxcervantes3srv' ? 60.GB
+        : params.hostname == 'vlinuxcervantes4srv' ? 120.GB
+        : System.err.println("\nERROR: unknown machine. Update incliva.config on nf-core/configs if you are working on another host.\n")
+    max_cpus = params.hostname == 'vlinuxcervantes3srv' ? 15
+        : params.hostname == 'vlinuxcervantes4srv' ? 19
+        : System.err.println("\nERROR: unknown machine. Update incliva.config on nf-core/configs if you are working on another host.\n")
 
     warning_message = {
         System.out.println("WARNING: !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!")
@@ -19,53 +26,9 @@ params {
     }.call()
 }
 
-// Function to get hostname
-def getHostname() {
-    def process = 'hostname'.execute()
-    process.waitFor()
-    return process.text.trim()
-}
-
-// Function to set singularity path according to which host nextflow is running on
-
-def hostname = { getHostname() }
-
-if (hostname == 'vlinuxcervantes3srv') {
-    System.out.println("\nINFO: working on ${hostname}\n")
-
-    // Resources details
-    params.max_memory = 60.GB
-    params.max_cpus = 15
-    singularity.cacheDir =  "/nfs/home/software/singularity/nf_cacheDir"
-
-    process {
-        resourceLimits = [
-            memory: 60.GB,
-            cpus: 15,
-        ]
-    }
-
-} else if (hostname == 'vlinuxcervantes4srv') {
-    System.out.println("\nINFO: working on ${hostname}.\n")
-
-    // Resources details
-    params.max_memory = 120.GB
-    params.max_cpus = 19
-    singularity.cacheDir = "/nfs/home/software/singularity/nf_cacheDir"
-
-    process {
-        resourceLimits = [
-            memory: 120.GB,
-            cpus: 19,
-        ]
-    }
-
-} else {
-    System.err.println("\nERROR: unknown machine. Update incliva.config on nf-core/configs if you are working on another host.\n")
-}
-
 // Singularity details
 singularity {
+    cacheDir = "/nfs/home/software/singularity/nf_cacheDir"
     enabled = true
     autoMounts = true
 }
@@ -74,4 +37,8 @@ singularity {
 process {
     executor = 'local'
     maxRetries = 2
+    resourceLimits = params.max_memory && params.max_cpus ? [
+        memory: params.max_memory,
+        cpus: params.max_cpus
+    ] : System.err.println("\nERROR: unknown machine. Update incliva.config on nf-core/configs if you are working on another host.\n")
 }
diff --git a/conf/kaust.config b/conf/kaust.config
index ba84b531c..bd0c39128 100755
--- a/conf/kaust.config
+++ b/conf/kaust.config
@@ -8,7 +8,7 @@ params {
 }
 
 // Load genome resources and assets hosted by the Bioinformatics team on IBEX cluster
-includeConfig 'https://raw.githubusercontent.com/bioinfo-kaust/references/refs/heads/main/configs/genomes.config'
+includeConfig (!System.getenv('NXF_OFFLINE') ? "https://raw.githubusercontent.com/bioinfo-kaust/references/refs/heads/main/configs/genomes.config" : "/dev/null")
 
 singularity {
     enabled = true
@@ -17,7 +17,7 @@ singularity {
     // Use existing images from the centralized library, if available
     libraryDir = "/biocorelab/BIX/resources/singularity/images/"
     // Download images that are missing from the library to user space
-    cacheDir = "/ibex/user/$USER/.singularity/nf_images/"
+    cacheDir = "/ibex/user/${System.getenv('USER')}/.singularity/nf_images/"
 }
 
 process {
diff --git a/conf/nci_gadi.config b/conf/nci_gadi.config
index bf3e1b08d..1b09d241b 100644
--- a/conf/nci_gadi.config
+++ b/conf/nci_gadi.config
@@ -4,6 +4,7 @@ params {
     config_profile_contact = 'Georgie Samaha (@georgiesamaha), Matthew Downton (@mattdton)'
     config_profile_url = 'https://opus.nci.org.au/display/Help/Gadi+User+Guide'
     project = System.getenv("PROJECT")
+    trace_timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')
 }
 
 // Enable use of Singularity to run containers
@@ -34,10 +35,9 @@ process {
 }
 
 // Write custom trace file with outputs required for SU calculation
-def trace_timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')
 trace {
     enabled = true
     overwrite = false
-    file = "./gadi-nf-core-trace-${trace_timestamp}.txt"
+    file = "./gadi-nf-core-trace-${params.trace_timestamp}.txt"
     fields = 'name,status,exit,duration,realtime,cpus,%cpu,memory,%mem,rss'
 }
diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config
index d96b1306e..b9ca79489 100644
--- a/conf/pipeline/eager/eva.config
+++ b/conf/pipeline/eager/eva.config
@@ -1,5 +1,10 @@
 // Profile config names for nf-core/configs
 
+validation.ignoreParams = [
+    'eager_eva_check_max_func'
+]
+
+
 params {
     // Specific nf-core/configs params
     config_profile_contact     = 'James Fellows Yates (@jfy133)'
@@ -21,44 +26,44 @@ process {
     clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" }
 
     withLabel: sc_tiny {
-        cpus   = { check_max(1, 'cpus') }
-        memory = { check_max(1.GB * task.attempt, 'memory') }
+        cpus   = { params.eager_eva_check_max_func(1, 'cpus') }
+        memory = { params.eager_eva_check_max_func(1.GB * task.attempt, 'memory') }
         time   = '365.d'
     }
 
     withLabel: sc_small {
-        cpus   = { check_max(1, 'cpus') }
-        memory = { check_max(4.GB * task.attempt, 'memory') }
+        cpus   = { params.eager_eva_check_max_func(1, 'cpus') }
+        memory = { params.eager_eva_check_max_func(4.GB * task.attempt, 'memory') }
         time   = '365.d'
     }
 
     withLabel: sc_medium {
-        cpus   = { check_max(1, 'cpus') }
-        memory = { check_max(8.GB * task.attempt, 'memory') }
+        cpus   = { params.eager_eva_check_max_func(1, 'cpus') }
+        memory = { params.eager_eva_check_max_func(8.GB * task.attempt, 'memory') }
         time   = '365.d'
     }
 
     withLabel: mc_small {
-        cpus   = { check_max(2, 'cpus') }
-        memory = { check_max(4.GB * task.attempt, 'memory') }
+        cpus   = { params.eager_eva_check_max_func(2, 'cpus') }
+        memory = { params.eager_eva_check_max_func(4.GB * task.attempt, 'memory') }
         time   = '365.d'
     }
 
     withLabel: mc_medium {
-        cpus   = { check_max(4, 'cpus') }
-        memory = { check_max(8.GB * task.attempt, 'memory') }
+        cpus   = { params.eager_eva_check_max_func(4, 'cpus') }
+        memory = { params.eager_eva_check_max_func(8.GB * task.attempt, 'memory') }
         time   = '365.d'
     }
 
     withLabel: mc_large {
-        cpus   = { check_max(8, 'cpus') }
-        memory = { check_max(16.GB * task.attempt, 'memory') }
+        cpus   = { params.eager_eva_check_max_func(8, 'cpus') }
+        memory = { params.eager_eva_check_max_func(16.GB * task.attempt, 'memory') }
         time   = '365.d'
     }
 
     withLabel: mc_huge {
-        cpus   = { check_max(32, 'cpus') }
-        memory = { check_max(256.GB * task.attempt, 'memory') }
+        cpus   = { params.eager_eva_check_max_func(32, 'cpus') }
+        memory = { params.eager_eva_check_max_func(256.GB * task.attempt, 'memory') }
         time   = '365.d'
     }
 
@@ -115,7 +120,7 @@ process {
 
     withName: markduplicates {
         clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
-        memory         = { check_max(20.GB * task.attempt, 'memory') }
+        memory         = { params.eager_eva_check_max_func(20.GB * task.attempt, 'memory') }
         errorStrategy  = { task.exitStatus in [1, 143, 137, 104, 134, 139, 140] ? 'retry' : 'finish' }
     }
 
@@ -129,7 +134,7 @@ process {
 
     withName: additional_library_merge {
         clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
-        memory         = { check_max(4.GB * task.attempt, 'memory') }
+        memory         = { params.eager_eva_check_max_func(4.GB * task.attempt, 'memory') }
     }
 
     withName: metagenomic_complexity_filter {
@@ -138,8 +143,8 @@ process {
 
     withName: malt {
         clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G" }
-        cpus           = { check_max(32, 'cpus') }
-        memory         = { check_max(955.GB * task.attempt, 'memory') }
+        cpus           = { params.eager_eva_check_max_func(32, 'cpus') }
+        memory         = { params.eager_eva_check_max_func(955.GB * task.attempt, 'memory') }
     }
 
     withName: maltextract {
@@ -169,7 +174,7 @@ process {
 
     withName: damageprofiler {
         clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
-        memory         = { check_max(8.GB * task.attempt, 'memory') }
+        memory         = { params.eager_eva_check_max_func(8.GB * task.attempt, 'memory') }
         errorStrategy  = { task.exitStatus in [1, 143, 137, 104, 134, 139, 140] ? 'retry' : 'finish' }
     }
 
@@ -237,38 +242,38 @@ profiles {
             clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" }
 
             withLabel: sc_tiny {
-                cpus   = { check_max(1, 'cpus') }
-                memory = { check_max(1.5.GB * task.attempt, 'memory') }
+                cpus   = { params.eager_eva_check_max_func(1, 'cpus') }
+                memory = { params.eager_eva_check_max_func(1.5.GB * task.attempt, 'memory') }
             }
 
             withLabel: sc_small {
-                cpus   = { check_max(1, 'cpus') }
-                memory = { check_max(6.GB * task.attempt, 'memory') }
+                cpus   = { params.eager_eva_check_max_func(1, 'cpus') }
+                memory = { params.eager_eva_check_max_func(6.GB * task.attempt, 'memory') }
             }
 
             withLabel: sc_medium {
-                cpus   = { check_max(1, 'cpus') }
-                memory = { check_max(12.GB * task.attempt, 'memory') }
+                cpus   = { params.eager_eva_check_max_func(1, 'cpus') }
+                memory = { params.eager_eva_check_max_func(12.GB * task.attempt, 'memory') }
             }
 
             withLabel: mc_small {
-                cpus   = { check_max(2, 'cpus') }
-                memory = { check_max(6.GB * task.attempt, 'memory') }
+                cpus   = { params.eager_eva_check_max_func(2, 'cpus') }
+                memory = { params.eager_eva_check_max_func(6.GB * task.attempt, 'memory') }
             }
 
             withLabel: mc_medium {
-                cpus   = { check_max(4, 'cpus') }
-                memory = { check_max(12.GB * task.attempt, 'memory') }
+                cpus   = { params.eager_eva_check_max_func(4, 'cpus') }
+                memory = { params.eager_eva_check_max_func(12.GB * task.attempt, 'memory') }
             }
 
             withLabel: mc_large {
-                cpus   = { check_max(8, 'cpus') }
-                memory = { check_max(24.GB * task.attempt, 'memory') }
+                cpus   = { params.eager_eva_check_max_func(8, 'cpus') }
+                memory = { params.eager_eva_check_max_func(24.GB * task.attempt, 'memory') }
             }
 
             withLabel: mc_huge {
-                cpus   = { check_max(32, 'cpus') }
-                memory = { check_max(256.GB * task.attempt, 'memory') }
+                cpus   = { params.eager_eva_check_max_func(32, 'cpus') }
+                memory = { params.eager_eva_check_max_func(256.GB * task.attempt, 'memory') }
             }
 
             // Fixes for SGE and Java incompatibility due to  (and also some samtools?!) using more memory than you tell it to use
@@ -308,7 +313,7 @@ profiles {
 
             withName: markduplicates {
                 clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
-                memory         = { check_max(32.GB * task.attempt, 'memory') }
+                memory         = { params.eager_eva_check_max_func(32.GB * task.attempt, 'memory') }
                 errorStrategy  = { task.exitStatus in [1, 143, 137, 104, 134, 139, 140] ? 'retry' : 'finish' }
             }
 
@@ -322,7 +327,7 @@ profiles {
 
             withName: additional_library_merge {
                 clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
-                memory         = { check_max(4.GB * task.attempt, 'memory') }
+                memory         = { params.eager_eva_check_max_func(4.GB * task.attempt, 'memory') }
             }
 
             withName: metagenomic_complexity_filter {
@@ -331,13 +336,13 @@ profiles {
 
             withName: malt {
                 clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G" }
-                cpus           = { check_max(32, 'cpus') }
-                memory         = { check_max(955.GB * task.attempt, 'memory') }
+                cpus           = { params.eager_eva_check_max_func(32, 'cpus') }
+                memory         = { params.eager_eva_check_max_func(955.GB * task.attempt, 'memory') }
                 errorStrategy  = { task.exitStatus in [1, 143, 137, 104, 134, 139, 140] ? 'retry' : 'finish' }
             }
 
             withName: hostremoval_input_fastq {
-                memory = { check_max(32.GB * task.attempt, 'memory') }
+                memory = { params.eager_eva_check_max_func(32.GB * task.attempt, 'memory') }
             }
 
             withName: maltextract {
@@ -367,7 +372,7 @@ profiles {
 
             withName: damageprofiler {
                 clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
-                memory         = { check_max(16.GB * task.attempt, 'memory') }
+                memory         = { params.eager_eva_check_max_func(16.GB * task.attempt, 'memory') }
                 errorStrategy  = { task.exitStatus in [1, 143, 137, 104, 134, 139, 140] ? 'retry' : 'finish' }
             }
 
@@ -418,38 +423,38 @@ profiles {
             clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" }
 
             withLabel: sc_tiny {
-                cpus   = { check_max(1, 'cpus') }
-                memory = { check_max(2.GB * task.attempt, 'memory') }
+                cpus   = { params.eager_eva_check_max_func(1, 'cpus') }
+                memory = { params.eager_eva_check_max_func(2.GB * task.attempt, 'memory') }
             }
 
             withLabel: sc_small {
-                cpus   = { check_max(1, 'cpus') }
-                memory = { check_max(8.GB * task.attempt, 'memory') }
+                cpus   = { params.eager_eva_check_max_func(1, 'cpus') }
+                memory = { params.eager_eva_check_max_func(8.GB * task.attempt, 'memory') }
             }
 
             withLabel: sc_medium {
-                cpus   = { check_max(1, 'cpus') }
-                memory = { check_max(16.GB * task.attempt, 'memory') }
+                cpus   = { params.eager_eva_check_max_func(1, 'cpus') }
+                memory = { params.eager_eva_check_max_func(16.GB * task.attempt, 'memory') }
             }
 
             withLabel: mc_small {
-                cpus   = { check_max(2, 'cpus') }
-                memory = { check_max(8.GB * task.attempt, 'memory') }
+                cpus   = { params.eager_eva_check_max_func(2, 'cpus') }
+                memory = { params.eager_eva_check_max_func(8.GB * task.attempt, 'memory') }
             }
 
             withLabel: mc_medium {
-                cpus   = { check_max(4, 'cpus') }
-                memory = { check_max(16.GB * task.attempt, 'memory') }
+                cpus   = { params.eager_eva_check_max_func(4, 'cpus') }
+                memory = { params.eager_eva_check_max_func(16.GB * task.attempt, 'memory') }
             }
 
             withLabel: mc_large {
-                cpus   = { check_max(8, 'cpus') }
-                memory = { check_max(32.GB * task.attempt, 'memory') }
+                cpus   = { params.eager_eva_check_max_func(8, 'cpus') }
+                memory = { params.eager_eva_check_max_func(32.GB * task.attempt, 'memory') }
             }
 
             withLabel: mc_huge {
-                cpus   = { check_max(32, 'cpus') }
-                memory = { check_max(512.GB * task.attempt, 'memory') }
+                cpus   = { params.eager_eva_check_max_func(32, 'cpus') }
+                memory = { params.eager_eva_check_max_func(512.GB * task.attempt, 'memory') }
             }
 
             // Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use
@@ -489,13 +494,13 @@ profiles {
 
             withName: markduplicates {
                 clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
-                memory         = { check_max(48.GB * task.attempt, 'memory') }
+                memory         = { params.eager_eva_check_max_func(48.GB * task.attempt, 'memory') }
                 errorStrategy  = { task.exitStatus in [1, 143, 137, 104, 134, 139, 140] ? 'retry' : 'finish' }
             }
 
             withName: library_merge {
                 clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
-                memory         = { check_max(6.GB * task.attempt, 'memory') }
+                memory         = { params.eager_eva_check_max_func(6.GB * task.attempt, 'memory') }
             }
 
             withName: seqtype_merge {
@@ -504,11 +509,11 @@ profiles {
 
             withName: additional_library_merge {
                 clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
-                memory         = { check_max(6.GB * task.attempt, 'memory') }
+                memory         = { params.eager_eva_check_max_func(6.GB * task.attempt, 'memory') }
             }
 
             withName: hostremoval_input_fastq {
-                memory = { check_max(32.GB * task.attempt, 'memory') }
+                memory = { params.eager_eva_check_max_func(32.GB * task.attempt, 'memory') }
             }
 
             withName: metagenomic_complexity_filter {
@@ -517,8 +522,8 @@ profiles {
 
             withName: malt {
                 clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G" }
-                cpus           = { check_max(32, 'cpus') }
-                memory         = { check_max(955.GB * task.attempt, 'memory') }
+                cpus           = { params.eager_eva_check_max_func(32, 'cpus') }
+                memory         = { params.eager_eva_check_max_func(955.GB * task.attempt, 'memory') }
                 errorStrategy  = { task.exitStatus in [1, 143, 137, 104, 134, 139, 140] ? 'retry' : 'finish' }
             }
 
@@ -549,7 +554,7 @@ profiles {
 
             withName: damageprofiler {
                 clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
-                memory         = { check_max(32.GB * task.attempt, 'memory') }
+                memory         = { params.eager_eva_check_max_func(32.GB * task.attempt, 'memory') }
                 errorStrategy  = { task.exitStatus in [1, 143, 137, 104, 134, 139, 140] ? 'retry' : 'finish' }
             }
 
@@ -627,31 +632,31 @@ profiles {
 // Function to ensure that resource requirements don't go beyond
 // a maximum limit
 // FOR DSL1 PIPELINE ONLY!
-def check_max(obj, type) {
+params.eager_eva_check_max_func = { 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
+            if (obj.compareTo(params.max_memory as MemoryUnit) == 1)
+                return params.max_memory as MemoryUnit
             else
                 return obj
-        } catch (all) {
+        } catch (_) {
             println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
             return obj
         }
     } else if (type == 'time') {
         try {
-            if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
-                return params.max_time as nextflow.util.Duration
+            if (obj.compareTo(params.max_time as Duration) == 1)
+                return params.max_time as Duration
             else
                 return obj
-        } catch (all) {
+        } catch (_) {
             println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
             return obj
         }
     } else if (type == 'cpus') {
         try {
             return Math.min( obj, params.max_cpus as int )
-        } catch (all) {
+        } catch (_) {
             println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
             return obj
         }
diff --git a/conf/pipeline/eager/maestro.config b/conf/pipeline/eager/maestro.config
index 3db94b099..8ffca42a6 100644
--- a/conf/pipeline/eager/maestro.config
+++ b/conf/pipeline/eager/maestro.config
@@ -5,6 +5,12 @@
  * nextflow run nf-core/eager -profile maestro,<qos>,maestro,<genome> (where <qos> is long or normal and <genome> is nuclear, mitocondrial or unlimitedtime)
  */
 
+validation {
+    ignoreParams = [
+        'eager_maestro_check_max_func'
+    ]
+}
+
 params {
     config_profile_name        = 'nf-core/eager nuclear/mitocondrial - human profiles'
     config_profile_description = "Simple profiles for assessing computational ressources that fit human nuclear dna, human mitogenomes processing. unlimitedtime is also available "
@@ -32,41 +38,41 @@ profiles {
             maxRetries    = 2
 
             withName: makeBWAIndex {
-                cpus   = { check_max(8 * task.attempt, 'cpus') }
-                memory = { check_max(8.GB * task.attempt, 'memory') }
-                time   = { check_max(12.h * task.attempt, 'time') }
+                cpus   = { params.eager_maestro_check_max_func(8 * task.attempt, 'cpus') }
+                memory = { params.eager_maestro_check_max_func(8.GB * task.attempt, 'memory') }
+                time   = { params.eager_maestro_check_max_func(12.h * task.attempt, 'time') }
             }
             withName: adapter_removal {
-                cpus   = { check_max(8 * task.attempt, 'cpus') }
-                memory = { check_max(16.GB * task.attempt, 'memory') }
-                time   = { check_max(12.h * task.attempt, 'time') }
+                cpus   = { params.eager_maestro_check_max_func(8 * task.attempt, 'cpus') }
+                memory = { params.eager_maestro_check_max_func(16.GB * task.attempt, 'memory') }
+                time   = { params.eager_maestro_check_max_func(12.h * task.attempt, 'time') }
             }
             withName: bwa {
-                cpus   = { check_max(40 * task.attempt, 'cpus') }
-                memory = { check_max(40.GB * task.attempt, 'memory') }
+                cpus   = { params.eager_maestro_check_max_func(40 * task.attempt, 'cpus') }
+                memory = { params.eager_maestro_check_max_func(40.GB * task.attempt, 'memory') }
                 time   = 24.h
                 cache  = 'deep'
             }
             withName: markduplicates {
                 errorStrategy = { task.exitStatus in [143, 137, 104, 134, 139] ? 'retry' : 'finish' }
-                cpus          = { check_max(16 * task.attempt, 'cpus') }
-                memory        = { check_max(16.GB * task.attempt, 'memory') }
-                time          = { check_max(12.h * task.attempt, 'time') }
+                cpus          = { params.eager_maestro_check_max_func(16 * task.attempt, 'cpus') }
+                memory        = { params.eager_maestro_check_max_func(16.GB * task.attempt, 'memory') }
+                time          = { params.eager_maestro_check_max_func(12.h * task.attempt, 'time') }
             }
             withName: damageprofiler {
                 cpus   = 1
-                memory = { check_max(8.GB * task.attempt, 'memory') }
-                time   = { check_max(6.h * task.attempt, 'time') }
+                memory = { params.eager_maestro_check_max_func(8.GB * task.attempt, 'memory') }
+                time   = { params.eager_maestro_check_max_func(6.h * task.attempt, 'time') }
             }
             withName: fastp {
                 cpus   = 8
-                memory = { check_max(8.GB * task.attempt, 'memory') }
-                time   = { check_max(6.h * task.attempt, 'time') }
+                memory = { params.eager_maestro_check_max_func(8.GB * task.attempt, 'memory') }
+                time   = { params.eager_maestro_check_max_func(6.h * task.attempt, 'time') }
             }
             withName: fastqc {
                 cpus   = 2
-                memory = { check_max(8.GB * task.attempt, 'memory') }
-                time   = { check_max(6.h * task.attempt, 'time') }
+                memory = { params.eager_maestro_check_max_func(8.GB * task.attempt, 'memory') }
+                time   = { params.eager_maestro_check_max_func(6.h * task.attempt, 'time') }
             }
         }
     }
@@ -77,40 +83,40 @@ profiles {
             maxRetries    = 2
 
             withName: makeBWAIndex {
-                cpus   = { check_max(8 * task.attempt, 'cpus') }
-                memory = { check_max(8.GB * task.attempt, 'memory') }
-                time   = { check_max(12.h * task.attempt, 'time') }
+                cpus   = { params.eager_maestro_check_max_func(8 * task.attempt, 'cpus') }
+                memory = { params.eager_maestro_check_max_func(8.GB * task.attempt, 'memory') }
+                time   = { params.eager_maestro_check_max_func(12.h * task.attempt, 'time') }
             }
             withName: adapter_removal {
-                cpus   = { check_max(8 * task.attempt, 'cpus') }
-                memory = { check_max(16.GB * task.attempt, 'memory') }
-                time   = { check_max(12.h * task.attempt, 'time') }
+                cpus   = { params.eager_maestro_check_max_func(8 * task.attempt, 'cpus') }
+                memory = { params.eager_maestro_check_max_func(16.GB * task.attempt, 'memory') }
+                time   = { params.eager_maestro_check_max_func(12.h * task.attempt, 'time') }
             }
             withName: bwa {
-                cpus   = { check_max(5 * task.attempt, 'cpus') }
-                memory = { check_max(5.GB * task.attempt, 'memory') }
+                cpus   = { params.eager_maestro_check_max_func(5 * task.attempt, 'cpus') }
+                memory = { params.eager_maestro_check_max_func(5.GB * task.attempt, 'memory') }
                 time   = 24.h
             }
             withName: markduplicates {
                 errorStrategy = { task.exitStatus in [143, 137, 104, 134, 139] ? 'retry' : 'finish' }
-                cpus          = { check_max(5 * task.attempt, 'cpus') }
-                memory        = { check_max(5.GB * task.attempt, 'memory') }
-                time          = { check_max(6.h * task.attempt, 'time') }
+                cpus          = { params.eager_maestro_check_max_func(5 * task.attempt, 'cpus') }
+                memory        = { params.eager_maestro_check_max_func(5.GB * task.attempt, 'memory') }
+                time          = { params.eager_maestro_check_max_func(6.h * task.attempt, 'time') }
             }
             withName: damageprofiler {
                 cpus   = 1
-                memory = { check_max(5.GB * task.attempt, 'memory') }
-                time   = { check_max(3.h * task.attempt, 'time') }
+                memory = { params.eager_maestro_check_max_func(5.GB * task.attempt, 'memory') }
+                time   = { params.eager_maestro_check_max_func(3.h * task.attempt, 'time') }
             }
             withName: fastp {
                 cpus   = 8
-                memory = { check_max(5.GB * task.attempt, 'memory') }
-                time   = { check_max(3.h * task.attempt, 'time') }
+                memory = { params.eager_maestro_check_max_func(5.GB * task.attempt, 'memory') }
+                time   = { params.eager_maestro_check_max_func(3.h * task.attempt, 'time') }
             }
             withName: fastqc {
                 cpus   = 2
-                memory = { check_max(8.GB * task.attempt, 'memory') }
-                time   = { check_max(6.h * task.attempt, 'time') }
+                memory = { params.eager_maestro_check_max_func(8.GB * task.attempt, 'memory') }
+                time   = { params.eager_maestro_check_max_func(6.h * task.attempt, 'time') }
             }
         }
     }
@@ -128,31 +134,31 @@ profiles {
 // Function to ensure that resource requirements don't go beyond
 // a maximum limit
 // FOR DSL1 PIPELINE ONLY!
-def check_max(obj, type) {
+params.eager_maestro_check_max_func = { 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
+            if (obj.compareTo(params.max_memory as MemoryUnit) == 1)
+                return params.max_memory as MemoryUnit
             else
                 return obj
-        } catch (all) {
+        } catch (_) {
             println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
             return obj
         }
     } else if (type == 'time') {
         try {
-            if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
-                return params.max_time as nextflow.util.Duration
+            if (obj.compareTo(params.max_time as Duration) == 1)
+                return params.max_time as Duration
             else
                 return obj
-        } catch (all) {
+        } catch (_) {
             println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
             return obj
         }
     } else if (type == 'cpus') {
         try {
             return Math.min( obj, params.max_cpus as int )
-        } catch (all) {
+        } catch (_) {
             println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
             return obj
         }
diff --git a/conf/pipeline/methylseq/ku_sund_danhead.config b/conf/pipeline/methylseq/ku_sund_danhead.config
index 872cab827..1e1ebd95e 100644
--- a/conf/pipeline/methylseq/ku_sund_danhead.config
+++ b/conf/pipeline/methylseq/ku_sund_danhead.config
@@ -11,6 +11,6 @@ process {
         stageInMode = 'copy'
     }
     withName: 'NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_ALIGN' {
-        multicore = 1
+        ext.args = '--multicore 1'
     }
 }
diff --git a/conf/pipeline/proteinfold/nci_gadi.config b/conf/pipeline/proteinfold/nci_gadi.config
index f07999c01..b82bb4620 100644
--- a/conf/pipeline/proteinfold/nci_gadi.config
+++ b/conf/pipeline/proteinfold/nci_gadi.config
@@ -12,8 +12,6 @@ profiles {
         // Define process resource limits
         process {
             executor = 'pbspro'
-            project = System.getenv("PROJECT")
-            storage = params.storage_account?.trim() ? params.storage_account : "scratch/${params.project}+gdata/${params.project}"
             module = 'singularity'
             cache = 'lenient'
             stageInMode = 'symlink'
@@ -22,7 +20,6 @@ profiles {
             withName: 'RUN_ALPHAFOLD2|RUN_ALPHAFOLD2_PRED|RUN_ALPHAFOLD2_MSA' {
                 queue   = params.use_gpu ? 'gpuvolta' : 'normal'
                 cpus    = 48
-                gpus    = 4
                 time    = '4h'
                 memory  = 380.GB
             }
@@ -31,7 +28,6 @@ profiles {
                 container = "nf-core/proteinfold_colabfold:1.1.1"
                 queue     = params.use_gpu ? 'gpuvolta' : 'normal'
                 cpus      = 48
-                gpus      = 4
                 time      = '4h'
                 memory    = 380.GB
             }
@@ -40,18 +36,16 @@ profiles {
                 container = "nf-core/proteinfold_esmfold:1.1.1"
                 queue     = params.use_gpu ? 'gpuvolta' : 'normal'
                 cpus      = 48
-                gpus      = 4
                 time      = '4h'
                 memory    = 380.GB
             }
         }
 
         // Write custom trace file with outputs required for SU calculation
-        def trace_timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')
         trace {
             enabled = true
             overwrite = false
-            file = "./gadi-nf-core-trace-${trace_timestamp}.txt"
+            file = "./gadi-nf-core-trace-${new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')}.txt"
             fields = 'name,status,exit,duration,realtime,cpus,%cpu,memory,%mem,rss'
         }
     }
diff --git a/conf/pipeline/sarek/cfc.config b/conf/pipeline/sarek/cfc.config
index b7db254a5..db1c39d4e 100644
--- a/conf/pipeline/sarek/cfc.config
+++ b/conf/pipeline/sarek/cfc.config
@@ -1,5 +1,7 @@
 // Profile config names for nf-core/configs
 
+validation.ignoreParams = ['sarek_cfc_check_resource_func']
+
 params {
     // Specific nf-core/configs params
     config_profile_contact = 'Friederike Hanssen (@FriederikeHanssen)'
diff --git a/conf/pipeline/sarek/icr_davros.config b/conf/pipeline/sarek/icr_davros.config
index 5e5607581..4caaff472 100644
--- a/conf/pipeline/sarek/icr_davros.config
+++ b/conf/pipeline/sarek/icr_davros.config
@@ -6,10 +6,6 @@
 process {
     errorStrategy = { task.exitStatus in [104, 134, 137, 139, 141, 143, 255] ? 'retry' : 'finish' }
     maxRetries    = 5
-    withName: MapReads {
-        memory = { check_resource(12.GB) }
-        time   = { check_resource(48.h * task.attempt) }
-    }
 }
 
 params {
diff --git a/conf/sage.config b/conf/sage.config
index 148b1c29f..5cc35c2ba 100644
--- a/conf/sage.config
+++ b/conf/sage.config
@@ -12,6 +12,9 @@ params {
     max_time                   = 240.h
     single_cpu_mem             = 6.GB
 
+    // Define dynamic scaling factors
+    exit_status_scaling = [143,137,104,134,139,247]
+
     warning_message = {
         System.out.println("WARNING: !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!")
         System.out.println("WARNING:")
@@ -60,47 +63,38 @@ process {
     // Enable retries globally for certain exit codes
     errorStrategy  = { task.attempt <= 5 ? 'retry' : 'finish' }
 
-    cpus           = { 1 * factor(task, 2) }
-    memory         = { 6.GB * factor(task, 1) }
-    time           = { 24.h * factor(task, 1) }
+    cpus           = { task.exitStatus in params.exit_status_scaling ? Math.ceil(task.attempt/2) : 1 }
+    memory         = { 6.GB * (task.exitStatus in params.exit_status_scaling ? task.attempt : 1) }
+    time           = { 24.h * (task.exitStatus in params.exit_status_scaling ? task.attempt : 1) }
 
     // Process-specific resource requirements
     withLabel: process_single {
-        cpus   = { 1 * factor(task, 2) }
-        memory = { 6.GB * factor(task, 1) }
-        time   = { 24.h * factor(task, 1) }
+        cpus   = { task.exitStatus in params.exit_status_scaling ? Math.ceil(task.attempt/2) : 1 }
+        memory = { 6.GB * (task.exitStatus in params.exit_status_scaling ? task.attempt : 1) }
+        time   = { 24.h * (task.exitStatus in params.exit_status_scaling ? task.attempt : 1) }
     }
     withLabel: process_low {
-        cpus   = { 2 * factor(task, 2) }
-        memory = { 12.GB * factor(task, 1) }
-        time   = { 24.h * factor(task, 1) }
+        cpus   = { 2 * (task.exitStatus in params.exit_status_scaling ? Math.ceil(task.attempt/2) : 1) }
+        memory = { 12.GB * (task.exitStatus in params.exit_status_scaling ? task.attempt : 1) }
+        time   = { 24.h * (task.exitStatus in params.exit_status_scaling ? task.attempt : 1) }
     }
     withLabel: process_medium {
-        cpus   = { 8 * factor(task, 2) }
-        memory = { 32.GB * factor(task, 1) }
-        time   = { 48.h * factor(task, 1) }
+        cpus   = { 8 * (task.exitStatus in params.exit_status_scaling ? Math.ceil(task.attempt/2) : 1) }
+        memory = { 32.GB * (task.exitStatus in params.exit_status_scaling ? task.attempt : 1) }
+        time   = { 48.h * (task.exitStatus in params.exit_status_scaling ? task.attempt : 1) }
     }
     withLabel: process_high {
-        cpus   = { 16 * factor(task, 2) }
-        memory = { 64.GB * factor(task, 1) }
-        time   = { 96.h * factor(task, 1) }
+        cpus   = { 16 * (task.exitStatus in params.exit_status_scaling ? Math.ceil(task.attempt/2) : 1) }
+        memory = { 64.GB * (task.exitStatus in params.exit_status_scaling ? task.attempt : 1) }
+        time   = { 96.h * (task.exitStatus in params.exit_status_scaling ? task.attempt : 1) }
     }
     withLabel: process_long {
-        time = { 96.h * factor(task, 1) }
+        time = { 96.h * (task.exitStatus in params.exit_status_scaling ? task.attempt : 1) }
     }
     withLabel: 'process_high_memory|memory_max' {
-        memory = { 128.GB * factor(task, 1) }
+        memory = { 128.GB * (task.exitStatus in params.exit_status_scaling ? task.attempt : 1) }
     }
     withLabel: cpus_max {
-        cpus = { 32 * factor(task, 2) }
-    }
-}
-
-// Function to finely control the increase of the resource allocation
-def factor(task, slow_factor = 1) {
-    if ( task.exitStatus in [143,137,104,134,139,247] ) {
-        return Math.ceil( task.attempt / slow_factor) as int
-    } else {
-        return 1 as int
+        cpus = { 32 * (task.exitStatus in params.exit_status_scaling ? Math.ceil(task.attempt/2) : 1) }
     }
 }
diff --git a/conf/seadragon.config b/conf/seadragon.config
index 5f3843a07..946655393 100644
--- a/conf/seadragon.config
+++ b/conf/seadragon.config
@@ -1,10 +1,16 @@
-//Profile config names for nf-core/configs
+// Profile config names for nf-core/configs
 params {
     config_profile_description = 'University of Texas at MD Anderson HPC cluster profile provided by nf-core/configs'
     config_profile_contact = 'Jiawei Gu'
     config_profile_contact_github = '@jiawku'
     config_profile_contact_email = 'jiawei.gu@mdanderson.org'
     config_profile_url = 'https://hpcweb.mdanderson.edu/'
+
+    // Define dynamic scaling factors
+    max_memory = 3900.GB // Maximum memory based on evhighmem nodes
+    max_cpus = 80        // Maximum CPUs based on E80 nodes
+    max_time = 504.h     // Maximum runtime for evlong queues
+    igenomes_base = '/rsrch3/scratch/reflib/REFLIB_data/AWS-iGenomes'
 }
 
 env {
@@ -33,12 +39,11 @@ executor {
     jobName = { "${task.process.split(':').last()}" }
 }
 
-
 process {
     resourceLimits = [
         memory: 3900.GB, // Max memory based on vhighmem node
-        cpus: 80,       // Max CPUs based on E80 node
-        time: 504.h     // Max time for long queues
+        cpus: 80,        // Max CPUs based on E80 node
+        time: 504.h      // Max time for long queues
     ]
 
     executor = 'lsf' // Use LSF executor
@@ -71,11 +76,4 @@ process {
     }
 }
 
-params {
-    max_memory = 3900.GB  // Maximum memory based on nodes
-    max_cpus = 80        // Maximum CPUs based on E80 nodes
-    max_time = 504.h     // Maximum runtime for evlong queues
-    igenomes_base = '/rsrch3/scratch/reflib/REFLIB_data/AWS-iGenomes'
-}
-
 cleanup = true
diff --git a/conf/utd_ganymede.config b/conf/utd_ganymede.config
index 5869eba65..ad4a319bb 100644
--- a/conf/utd_ganymede.config
+++ b/conf/utd_ganymede.config
@@ -1,4 +1,4 @@
-//Profile config names for nf-core/configs
+// Profile config names for nf-core/configs
 params {
     config_profile_description = 'University of Texas at Dallas HPC cluster profile provided by nf-core/configs'
     config_profile_contact = 'Edmund Miller'
@@ -8,32 +8,14 @@ params {
 }
 
 env {
-    SINGULARITY_CACHEDIR="/home/$USER/scratch/singularity"
+    SINGULARITY_CACHEDIR="/home/${System.getenv('USER')}/scratch/singularity"
 }
 
 singularity {
     enabled = true
     envWhitelist='SINGULARITY_BINDPATH,LD_LIBRARY_PATH'
     autoMounts = true
-    cacheDir = "/home/$USER/scratch/singularity"
-}
-
-def membership = "groups".execute().text
-def genomics_queue_memory = 28.GB
-
-def select_queue = { memory, cpu ->
-    if (memory <= genomics_queue_memory && cpu <= 16 && membership.contains('genomics')) {
-        return 'genomics,normal'
-    }
-    if (memory > genomics_queue_memory && memory <= 125.GB && cpu <= 12 && membership.contains('kim')) {
-        return 'Kim,128s'
-    }
-    if (memory > genomics_queue_memory && memory <= 125.GB && cpu <= 16) {
-        return '128s'
-    }
-    if (memory <= 250.GB && cpu <= 28) {
-        return '256i,256h'
-    }
+    cacheDir = "/home/${System.getenv('USER')}/scratch/singularity"
 }
 
 // Submit up to 100 concurrent jobs
@@ -54,7 +36,13 @@ process {
     ]
     beforeScript = 'module load singularity/3.2.1'
     executor = 'slurm'
-    queue = { select_queue(task.memory, task.cpu) }
+    queue = {
+        if (task.memory <= 28.GB && task.cpus <= 16 && "groups".execute().text.contains('genomics')) return 'genomics,normal'
+        if (task.memory > 28.GB && task.memory <= 125.GB && task.cpus <= 12 && "groups".execute().text.contains('kim')) return 'Kim,128s'
+        if (task.memory > 28.GB && task.memory <= params.queue_128s.memory && task.cpus <= 16) return '128s'
+        if (task.memory <= params.queue_256.memory && task.cpus <= 28) return '256i,256h'
+        throw new IllegalArgumentException("No matching queue for memory=${task.memory}, cpu=${task.cpus}")
+    }
 
     withLabel:process_medium {
         cpus   = 16
diff --git a/conf/utd_juno.config b/conf/utd_juno.config
index 373e5f6f1..d9588b6eb 100644
--- a/conf/utd_juno.config
+++ b/conf/utd_juno.config
@@ -1,3 +1,4 @@
+// Profile config names for nf-core/configs
 params {
     config_profile_description = 'University of Texas at Dallas HPC cluster profile provided by nf-core/configs'
     config_profile_contact = 'Anne Fu'
@@ -7,54 +8,13 @@ params {
 }
 
 env {
-    SINGULARITY_CACHEDIR="/home/$USER/scratch/singularity"
+    SINGULARITY_CACHEDIR="/home/${System.getenv('USER')}/scratch/singularity"
 }
 
-
-def select_queue_and_flags = { cpus, memory, time, accelerator ->
-    var accelerator_count = 0;
-    var accelerator_ty = null;
-    if (accelerator != null) {
-        if (accelerator instanceof Number) {
-            accelerator_count = accelerator;
-        } else if (accelerator instanceof Map) {
-            accelerator_ty = accelerator.type;
-            accelerator_count = accelerator.limit;
-        } else {
-            throw new IllegalArgumentException("Invalid `accelerator` directive value: $accelerator [${accelerator.getClass().getName()}]")
-        }
-    }
-
-    if (accelerator_count > 0) {
-        if (["h100", "nvidia_h100", "nvidia-h100",  "nvidia_h100_80gb_hbm3"].contains(accelerator_ty)) {
-            // if this is a long task with a single accelarator, probably need the whole GPU
-            if (accelerator_count == 1 && time >= 2.h) {
-                return ['queue': 'h100', 'flags': "--gres=nvidia_h100_80gb_hbm3=${accelerator_count}"];
-            } else {
-                return ['queue': 'h100-2.40gb', 'flags': "--gres=nvidia_h100_80gb_hbm3=${accelerator_count}"];
-            }
-        }
-
-        if (["a30", "nvidia_a30", "nvidia-a30", "nvidia_a30_2g", "nvidia_a30_4g"].contains(accelerator_ty)) {
-            if (accelerator_count >= 4) {
-                return ['queue': 'a30-4.6gb', 'flags': "--gres=nvidia_a30=${accelerator_count}"];
-            } else if (accelerator_count >= 2) {
-                return ['queue': 'a30-2.12gb', 'flags': "--gres=nvidia_a30_2g=${accelerator_count}"];
-            } else if (accelerator_count >= 1) {
-                return ['queue': 'a30', 'flags': "--gres=nvidia_a30_1g=${accelerator_count}"];
-            }
-        }
-    }
-
-    if (memory >= 384.GB && memory <= 512.GB) {
-        return ['queue': 'h100', 'flags': ""];
-    }
-
-    if (memory >= 512.GB) {
-        return ['queue': 'a30', 'flags': ""];
-    }
-
-    return ['queue': 'normal', 'flags': ''];
+singularity {
+    enabled = true
+    autoMounts = true
+    cacheDir = "/home/${System.getenv('USER')}/scratch/singularity"
 }
 
 executor {
@@ -64,19 +24,49 @@ executor {
     jobName = { "${task.process.split(':').last()}" }
 }
 
-singularity {
-    enabled = true
-    autoMounts = true
-    cacheDir = "/home/$USER/scratch/singularity"
-}
-
 process {
     executor = 'slurm'
     queue = {
-        select_queue_and_flags(task.cpus, task.memory, task.time, task.get('accelerator')).queue
+        if (task.get('accelerator')?.type in ['h100', 'nvidia_h100', 'nvidia-h100', 'nvidia_h100_80gb_hbm3']) {
+            if (task.get('accelerator')?.limit == 1 && task.time >= 2.h) {
+                return 'h100'
+            }
+            return 'h100-2.40gb'
+        }
+        if (task.get('accelerator')?.type in ['a30', 'nvidia_a30', 'nvidia-a30', 'nvidia_a30_2g', 'nvidia_a30_4g']) {
+            if (task.get('accelerator')?.limit >= 4) {
+                return 'a30-4.6gb'
+            }
+            if (task.get('accelerator')?.limit >= 2) {
+                return 'a30-2.12gb'
+            }
+            return 'a30'
+        }
+        if (task.memory >= 384.GB && task.memory <= 512.GB) {
+            return 'h100'
+        }
+        if (task.memory >= 512.GB) {
+            return 'a30'
+        }
+        return 'normal'
     }
     clusterOptions = {
-        select_queue_and_flags(task.cpus, task.memory, task.time, task.get('accelerator')).flags
+        if (task.get('accelerator')?.type in ['h100', 'nvidia_h100', 'nvidia-h100', 'nvidia_h100_80gb_hbm3']) {
+            if (task.get('accelerator')?.limit == 1 && task.time >= 2.h) {
+                return "--gres=nvidia_h100_80gb_hbm3=${task.get('accelerator')?.limit}"
+            }
+            return "--gres=nvidia_h100_80gb_hbm3=${task.get('accelerator')?.limit}"
+        }
+        if (task.get('accelerator')?.type in ['a30', 'nvidia_a30', 'nvidia-a30', 'nvidia_a30_2g', 'nvidia_a30_4g']) {
+            if (task.get('accelerator')?.limit >= 4) {
+                return "--gres=nvidia_a30=${task.get('accelerator')?.limit}"
+            }
+            if (task.get('accelerator')?.limit >= 2) {
+                return "--gres=nvidia_a30_2g=${task.get('accelerator')?.limit}"
+            }
+            return "--gres=nvidia_a30_1g=${task.get('accelerator')?.limit}"
+        }
+        return ''
     }
     withLabel: gpu {
         containerOptions = '--nv'
diff --git a/conf/vsc_kul_uhasselt.config b/conf/vsc_kul_uhasselt.config
index 152e2028c..9ccd2b059 100644
--- a/conf/vsc_kul_uhasselt.config
+++ b/conf/vsc_kul_uhasselt.config
@@ -1,9 +1,21 @@
+// Ignore configuration parameters in validation
+validation {
+    ignoreParams = [
+        'vsc_kul_hasselt_scratchdir',
+        'vsc_kul_hasselt_tier2_project',
+        'vsc_kul_hasselt_available_queues',
+        'vsc_kul_hasselt_publish_location',
+        'vsc_kul_hasselt_time_threshold',
+        'vsc_kul_hasselt_memory_threshold_genius',
+        'vsc_kul_hasselt_memory_threshold_wice',
+    ]
+}
+
 // Default to /tmp directory if $VSC_SCRATCH scratch env is not available,
 // see: https://github.com/nf-core/configs?tab=readme-ov-file#adding-a-new-config
-def SCRATCH_DIR      = System.getenv("VSC_SCRATCH") ?: "/tmp"
-def TIER2_PROJECT    = System.getenv("SLURM_ACCOUNT") ?: null
-def DEDICATED_QUEUES = System.getenv("VSC_DEDICATED_QUEUES") ?: ""
-def AVAILABLE_QUEUES = DEDICATED_QUEUES.toString().split(',')
+params.vsc_kul_hasselt_scratchdir       = System.getenv("VSC_SCRATCH") ?: "/tmp"
+params.vsc_kul_hasselt_tier2_project    = System.getenv("SLURM_ACCOUNT") ?: null
+params.vsc_kul_hasselt_available_queues = (System.getenv("VSC_DEDICATED_QUEUES") ?: "").toString().split(',')
 
 // Perform work directory cleanup when the run has succesfully completed
 // cleanup = true
@@ -29,7 +41,7 @@ process {
 singularity {
     enabled     = true
     autoMounts  = true
-    cacheDir    = "$SCRATCH_DIR/.singularity"
+    cacheDir    = "${params.vsc_kul_hasselt_scratchdir}/.singularity"
     pullTimeout = "30 min"
 }
 
@@ -38,28 +50,28 @@ params {
     config_profile_url         = 'https://docs.vscentrum.be/en/latest/index.html'
 }
 
-
-def publishLocation = params.get('outdir', "$launchDir")
-
-def co2_timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')
+params.vsc_kul_hasselt_publish_location = params.get('outdir', "$launchDir")
+params.vsc_kul_hasselt_co2_timestamp = params.containsKey('trace_report_suffix') ? params.trace_report_suffix : new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')
 
 co2footprint {
-    traceFile = "${publishLocation}/pipeline_info/co2footprint_trace_${co2_timestamp}.txt"
-    summaryFile = "${publishLocation}/pipeline_info/co2footprint_summary_${co2_timestamp}.txt"
-    reportFile = "${publishLocation}/pipeline_info/co2footprint_report_${co2_timestamp}.html"
+    traceFile = "${params.vsc_kul_hasselt_publish_location}/pipeline_info/co2footprint_trace_${params.vsc_kul_hasselt_co2_timestamp}.txt"
+    summaryFile = "${params.vsc_kul_hasselt_publish_location}/pipeline_info/co2footprint_summary_${params.vsc_kul_hasselt_co2_timestamp}.txt"
+    reportFile = "${params.vsc_kul_hasselt_publish_location}/pipeline_info/co2footprint_report_${params.vsc_kul_hasselt_co2_timestamp}.html"
     location = 'BE'
     //pue = 1.33                                   // replace with PUE of your data center
     machineType = 'compute cluster'             // set to 'compute cluster', 'local', or 'cloud'
 }
 
 env {
-    APPTAINER_TMPDIR="$SCRATCH_DIR/.apptainer/tmp"
-    APPTAINER_CACHEDIR="$SCRATCH_DIR/.apptainer/cache"
+    APPTAINER_TMPDIR="${params.vsc_kul_hasselt_scratchdir}/.apptainer/tmp"
+    APPTAINER_CACHEDIR="${params.vsc_kul_hasselt_scratchdir}/.apptainer/cache"
 }
 
 // AWS maximum retries for errors (This way the pipeline doesn't fail if the download fails one time)
 aws {
-    maxErrorRetry = 3
+    client {
+        maxErrorRetry = 3
+    }
 }
 
 /*
@@ -72,127 +84,13 @@ aws {
 /*
  * Constants:
  * ----------
- * TIME_THRESHOLD: 72 hours - Threshold for determining long-running jobs
- * MEMORY_THRESHOLD (GENIUS): 175GB - Memory threshold for bigmem queues
- * MEMORY_THRESHOLD (WICE): 239GB - Memory threshold for high-memory queues
-*/
-def TIME_THRESHOLD = 72.h
-def MEMORY_THRESHOLD_GENIUS = 175.GB
-def MEMORY_THRESHOLD_WICE = 239.GB
-
-/*
- * ---------
- * Functions:
- * ----------
- * These functions are designed to select the appropriate HPC queues of
- * VSC_KUL_UHASSELT based on task requirements. They handle both standard
- * and GPU queues, considering memory requirements, execution time, and
- * queue availability.
-*/
-
-/*
- * limitTaskTime(time, maxTime)
- *     Ensures task time doesn't exceed the maximum allowed time
- *     @param time Current task time
- *     @param maxTime Maximum allowed time
- *     @return Limited task time
-*/
-def limitTaskTime(time, maxTime) {
-    return time > maxTime ? maxTime : time
-}
-
-/*
- * determineGeniusQueue(task)
- *     Selects appropriate CPU queue for GENIUS cluster
- *     @param task Nextflow task object containing memory and time requirements
- *     @return Queue name based on task requirements
-*/
-def determineGeniusQueue = { task ->
-    def isHighMemory = task.memory >= MEMORY_THRESHOLD_GENIUS
-    def isLongRunning = task.time >= TIME_THRESHOLD
-    def hasDedicatedBigmem = AVAILABLE_QUEUES.contains('dedicated_big_bigmem')
-
-    if (isHighMemory) {
-        return isLongRunning ?
-            (hasDedicatedBigmem ? 'dedicated_big_bigmem' : 'bigmem_long') :
-            'bigmem'
-    }
-
-    return isLongRunning ? 'batch_long' : 'batch'
-}
-
-/*
- * determineGeniusGpuQueue(task)
- *     Selects appropriate GPU queue for GENIUS cluster
- *     @param task Nextflow task object containing memory and time requirements
- *     @return GPU queue name based on task requirements
-*/
-def determineGeniusGpuQueue = { task ->
-    def isHighMemory = task.memory >= MEMORY_THRESHOLD_GENIUS
-    def isLongRunning = task.time >= TIME_THRESHOLD
-    def hasDedicatedGpu = AVAILABLE_QUEUES.contains('dedicated_rega_gpu')
-    def hasAmdGpu = AVAILABLE_QUEUES.contains('amd')
-
-    if (isHighMemory) {
-        return isLongRunning ? 'gpu_v100_long' : 'gpu_v100'
-    }
-
-    if (isLongRunning) {
-        if (hasDedicatedGpu) return 'dedicated_rega_gpu'
-        if (hasAmdGpu) return 'amd_long'
-        return 'gpu_p100_long'
-    }
-
-    return hasAmdGpu ? 'amd' : 'gpu_p100'
-}
-
-/*
- * determineWiceQueue(task)
- *     Selects appropriate CPU queue for WICE cluster
- *     @param task Nextflow task object containing memory and time requirements
- *     @return Queue name based on task requirements and availability
+ * params.vsc_kul_hasselt_time_threshold: 72 hours - Threshold for determining long-running jobs
+ * params.vsc_kul_hasselt_memory_threshold_genius: 175GB - Memory threshold for bigmem queues
+ * params.vsc_kul_hasselt_memory_threshold_wice: 239GB - Memory threshold for high-memory queues
 */
-def determineWiceQueue = { task ->
-    def isHighMemory = task.memory >= MEMORY_THRESHOLD_WICE
-    def isLongRunning = task.time >= TIME_THRESHOLD
-    def hasDedicatedQueue = AVAILABLE_QUEUES.contains('dedicated_big_bigmem')
-
-    if (isHighMemory) {
-        if (isLongRunning && hasDedicatedQueue) {
-            return 'dedicated_big_bigmem'
-        }
-        task.time = limitTaskTime(task.time, TIME_THRESHOLD)
-        return 'bigmem,hugemem'
-    }
-
-    return isLongRunning ?
-        'batch_long,batch_icelake_long,batch_sapphirerapids_long' :
-        'batch,batch_sapphirerapids,batch_icelake'
-}
-
-/*
- * determineWiceGpuQueue(task)
- *     Selects appropriate GPU queue for WICE cluster
- *     @param task Nextflow task object containing memory and time requirements
- *     @return GPU queue name based on task requirements
-*/
-def determineWiceGpuQueue = { task ->
-    def isHighMemory = task.memory >= MEMORY_THRESHOLD_WICE
-    def isLongRunning = task.time >= TIME_THRESHOLD
-    def hasDedicatedQueue = isHighMemory ?
-        AVAILABLE_QUEUES.contains('dedicated_big_gpu_h100') :
-        AVAILABLE_QUEUES.contains('dedicated_big_gpu')
-
-    if (isLongRunning && !hasDedicatedQueue) {
-        task.time = limitTaskTime(task.time, TIME_THRESHOLD)
-    }
-
-    if (isHighMemory) {
-        return (isLongRunning && hasDedicatedQueue) ? 'dedicated_big_gpu_h100' : 'gpu_h100'
-    }
-
-    return (isLongRunning && hasDedicatedQueue) ? 'dedicated_big_gpu' : 'gpu_a100,gpu'
-}
+params.vsc_kul_hasselt_time_threshold = 72.h
+params.vsc_kul_hasselt_memory_threshold_genius = 175.GB
+params.vsc_kul_hasselt_memory_threshold_wice = 239.GB
 
 /*
  * ========
@@ -212,24 +110,54 @@ profiles {
 
         process {
             // 768 - 65 so 65GB for overhead, max is 720000MB
+            ext.vsc_kul_hasselt_queue = {
+                def isHighMemory = task.memory >= params.vsc_kul_hasselt_memory_threshold_genius
+                def isLongRunning = task.time >= params.vsc_kul_hasselt_time_threshold
+                def hasDedicatedBigmem = params.vsc_kul_hasselt_available_queues.contains('dedicated_big_bigmem')
+
+                if (isHighMemory) {
+                    return isLongRunning ?
+                        (hasDedicatedBigmem ? 'dedicated_big_bigmem' : 'bigmem_long') :
+                        'bigmem'
+                }
+
+                return isLongRunning ? 'batch_long' : 'batch'
+            }
             resourceLimits = [ memory: 703.GB, cpus: 36, time: 168.h ]
-            beforeScript   = { 'module load cluster/genius/' + determineGeniusQueue(task).toString().split(',')[0] }
-            queue          = { determineGeniusQueue(task) }
+            beforeScript   = { 'module load cluster/genius/' + task.ext.vsc_kul_hasselt_queue.toString().split(',')[0] }
+            queue          = { task.ext.vsc_kul_hasselt_queue }
             clusterOptions = {
-                determineGeniusQueue(task) =~ /dedicated/ ?
+                task.ext.vsc_kul_hasselt_queue =~ /dedicated/ ?
                     "--clusters=genius --account=lp_big_genius_cpu" :
-                    "--clusters=genius --account=$TIER2_PROJECT"
+                    "--clusters=genius --account=${params.vsc_kul_hasselt_tier2_project}"
             }
 
             withLabel: '.*gpu.*'{
+                ext.vsc_kul_hasselt_queue = {
+                    def isHighMemory = task.memory >= params.vsc_kul_hasselt_memory_threshold_genius
+                    def isLongRunning = task.time >= params.vsc_kul_hasselt_time_threshold
+                    def hasDedicatedGpu = params.vsc_kul_hasselt_available_queues.contains('dedicated_rega_gpu')
+                    def hasAmdGpu = params.vsc_kul_hasselt_available_queues.contains('amd')
+
+                    if (isHighMemory) {
+                        return isLongRunning ? 'gpu_v100_long' : 'gpu_v100'
+                    }
+
+                    if (isLongRunning) {
+                        if (hasDedicatedGpu) return 'dedicated_rega_gpu'
+                        if (hasAmdGpu) return 'amd_long'
+                        return 'gpu_p100_long'
+                    }
+
+                    return hasAmdGpu ? 'amd' : 'gpu_p100'
+                }
                 resourceLimits         = [ memory: 703.GB, cpus: 36 , time: 168.h ]
-                beforeScript           = { 'module load cluster/genius/' + determineGeniusGpuQueue(task).toString().split(',')[0] }
-                apptainer.runOptions   = '--containall --cleanenv --nv'
-                singularity.runOptions = '--containall --cleanenv --nv'
-                queue                  = { determineGeniusGpuQueue(task) }
+                beforeScript           = { 'module load cluster/genius/' + task.ext.vsc_kul_hasselt_queue.toString().split(',')[0] }
+                containerOptions       = '--containall --cleanenv --nv'
+                queue                  = { task.ext.vsc_kul_hasselt_queue }
                 clusterOptions         = {
                     def gpus = task.accelerator?.request ?: Math.max(1, Math.floor((task.cpus ?:1)/9) as int)
-                    "--gres=gpu:${gpus} --clusters=genius --account=$TIER2_PROJECT"
+                    "--gres=gpu:${gpus} --clusters=genius --account=${params.vsc_kul_hasselt_tier2_project}"
                 }
             }
         }
@@ -242,12 +170,30 @@ profiles {
 
         process {
             // 768 - 65 so 65GB for overhead, max is 720000MB
+            ext.vsc_kul_hasselt_queue = {
+                def isHighMemory = task.memory >= params.vsc_kul_hasselt_memory_threshold_genius
+                def isLongRunning = task.time >= params.vsc_kul_hasselt_time_threshold
+                def hasDedicatedGpu = params.vsc_kul_hasselt_available_queues.contains('dedicated_rega_gpu')
+                def hasAmdGpu = params.vsc_kul_hasselt_available_queues.contains('amd')
+
+                if (isHighMemory) {
+                    return isLongRunning ? 'gpu_v100_long' : 'gpu_v100'
+                }
+
+                if (isLongRunning) {
+                    if (hasDedicatedGpu) return 'dedicated_rega_gpu'
+                    if (hasAmdGpu) return 'amd_long'
+                    return 'gpu_p100_long'
+                }
+
+                return hasAmdGpu ? 'amd' : 'gpu_p100'
+            }
             resourceLimits = [ memory: 703.GB, cpus: 36, time: 168.h]
-            beforeScript   = { 'module load cluster/genius/' + determineGeniusGpuQueue(task).toString().split(',')[0] }
-            queue          = { determineGeniusGpuQueue(task) }
+            beforeScript   = { 'module load cluster/genius/' + task.ext.vsc_kul_hasselt_queue.toString().split(',')[0] }
+            queue          = { task.ext.vsc_kul_hasselt_queue }
             clusterOptions = {
                 def gpus = task.accelerator?.request ?: Math.max(1, Math.floor((task.cpus ?:1)/9) as int)
-                "--gres=gpu:${gpus} --clusters=genius --account=$TIER2_PROJECT"
+                "--gres=gpu:${gpus} --clusters=genius --account=${params.vsc_kul_hasselt_tier2_project}"
             }
         }
     }
@@ -257,27 +203,60 @@ profiles {
 
         process {
             // max is 2016000
+            ext.vsc_kul_hasselt_queue = {
+                def isHighMemory = task.memory >= params.vsc_kul_hasselt_memory_threshold_wice
+                def isLongRunning = task.time >= params.vsc_kul_hasselt_time_threshold
+                def hasDedicatedQueue = params.vsc_kul_hasselt_available_queues.contains('dedicated_big_bigmem')
+
+                if (isHighMemory) {
+                    if (isLongRunning && hasDedicatedQueue) {
+                        return 'dedicated_big_bigmem'
+                    }
+                    task.time = { task.time > params.vsc_kul_hasselt_time_threshold ? params.vsc_kul_hasselt_time_threshold : task.time }
+                    return 'bigmem,hugemem'
+                }
+
+                return isLongRunning ?
+                    'batch_long,batch_icelake_long,batch_sapphirerapids_long' :
+                    'batch,batch_sapphirerapids,batch_icelake'
+            }
             resourceLimits = [ memory: 1968.GB, cpus: 72, time: 168.h ]
-            beforeScript   = { 'module load cluster/wice/' + determineWiceQueue(task).toString().split(',')[0] }
-            queue          = { determineWiceQueue(task) }
+            beforeScript   = { 'module load cluster/wice/' + task.ext.vsc_kul_hasselt_queue.toString().split(',')[0] }
+            queue          = { task.ext.vsc_kul_hasselt_queue }
             clusterOptions = {
-                determineWiceQueue(task) =~ /dedicated/ ?
+                task.ext.vsc_kul_hasselt_queue =~ /dedicated/ ?
                     "--clusters=wice --account=lp_big_wice_cpu" :
-                    "--clusters=wice --account=$TIER2_PROJECT"
+                    "--clusters=wice --account=${params.vsc_kul_hasselt_tier2_project}"
             }
 
             withLabel: '.*gpu.*' {
+                ext.vsc_kul_hasselt_queue = {
+                    def isHighMemory = task.memory >= params.vsc_kul_hasselt_memory_threshold_wice
+                    def isLongRunning = task.time >= params.vsc_kul_hasselt_time_threshold
+                    def hasDedicatedQueue = isHighMemory ?
+                        params.vsc_kul_hasselt_available_queues.contains('dedicated_big_gpu_h100') :
+                        params.vsc_kul_hasselt_available_queues.contains('dedicated_big_gpu')
+
+                    if (isLongRunning && !hasDedicatedQueue) {
+                        task.time = { task.time > params.vsc_kul_hasselt_time_threshold ? params.vsc_kul_hasselt_time_threshold : task.time }
+                    }
+
+                    if (isHighMemory) {
+                        return (isLongRunning && hasDedicatedQueue) ? 'dedicated_big_gpu_h100' : 'gpu_h100'
+                    }
+
+                    return (isLongRunning && hasDedicatedQueue) ? 'dedicated_big_gpu' : 'gpu_a100,gpu'
+                }
                 resourceLimits         = [ memory: 703.GB, cpus: 64, time: 168.h ]
-                apptainer.runOptions   = '--containall --cleanenv --nv'
-                singularity.runOptions = '--containall --cleanenv --nv'
-                beforeScript           = { 'module load cluster/wice/' + determineWiceGpuQueue(task).toString().split(',')[0] }
-                queue                  = { determineWiceGpuQueue(task) }
+                containerOptions       = '--containall --cleanenv --nv'
+                beforeScript           = { 'module load cluster/wice/' + task.ext.vsc_kul_hasselt_queue.toString().split(',')[0] }
+                queue                  = { task.ext.vsc_kul_hasselt_queue }
                 clusterOptions         = {
                     def gpus = task.accelerator?.request ?: Math.max(1, Math.floor((task.cpus ?:1)/16) as int)
-                    def queueValue = determineWiceGpuQueue(task)
+                    def queueValue = task.ext.vsc_kul_hasselt_queue
                     queueValue =~ /dedicated_big_gpu_h100/ ? "--clusters=wice --account=lp_big_wice_gpu_h100 --gres=gpu:${gpus}" :
                     queueValue =~ /dedicated_big_gpu/ ? "--clusters=wice --account=lp_big_wice_gpu --gres=gpu:${gpus}" :
-                    "--clusters=wice --account=$TIER2_PROJECT --gres=gpu:${gpus}"
+                    "--clusters=wice --account=${params.vsc_kul_hasselt_tier2_project} --gres=gpu:${gpus}"
                 }
             }
         }
@@ -290,15 +269,32 @@ profiles {
 
         process {
             // 768 - 65 so 65GB for overhead, max is 720000MB
-            beforeScript   = { 'module load cluster/wice/' + determineWiceGpuQueue(task).toString().split(',')[0] }
+            ext.vsc_kul_hasselt_queue = {
+                def isHighMemory = task.memory >= params.vsc_kul_hasselt_memory_threshold_wice
+                def isLongRunning = task.time >= params.vsc_kul_hasselt_time_threshold
+                def hasDedicatedQueue = isHighMemory ?
+                    params.vsc_kul_hasselt_available_queues.contains('dedicated_big_gpu_h100') :
+                    params.vsc_kul_hasselt_available_queues.contains('dedicated_big_gpu')
+
+                if (isLongRunning && !hasDedicatedQueue) {
+                    task.time = { task.time > params.vsc_kul_hasselt_time_threshold ? params.vsc_kul_hasselt_time_threshold : task.time }
+                }
+
+                if (isHighMemory) {
+                    return (isLongRunning && hasDedicatedQueue) ? 'dedicated_big_gpu_h100' : 'gpu_h100'
+                }
+
+                return (isLongRunning && hasDedicatedQueue) ? 'dedicated_big_gpu' : 'gpu_a100,gpu'
+            }
+            beforeScript   = { 'module load cluster/wice/' + task.ext.vsc_kul_hasselt_queue.toString().split(',')[0] }
             resourceLimits = [ memory: 703.GB, cpus: 64, time: 168.h ]
-            queue          = { determineWiceGpuQueue(task) }
+            queue          = { task.ext.vsc_kul_hasselt_queue }
             clusterOptions = {
                 def gpus = task.accelerator?.request ?: Math.max(1, Math.floor((task.cpus ?:1)/16) as int)
-                def queueValue = determineWiceGpuQueue(task)
+                def queueValue = task.ext.vsc_kul_hasselt_queue
                 queueValue =~ /dedicated_big_gpu_h100/ ? "--clusters=wice --account=lp_big_wice_gpu_h100 --gres=gpu:${gpus}" :
                 queueValue =~ /dedicated_big_gpu/ ? "--clusters=wice --account=lp_big_wice_gpu --gres=gpu:${gpus}" :
-                "--clusters=wice --account=$TIER2_PROJECT --gres=gpu:${gpus}"
+                "--clusters=wice --account=${params.vsc_kul_hasselt_tier2_project} --gres=gpu:${gpus}"
             }
         }
     }
@@ -307,7 +303,7 @@ profiles {
         params.config_profile_description = 'superdome profile for use on the genius cluster of the VSC HPC.'
 
         process {
-            clusterOptions = {"--clusters=genius --account=$TIER2_PROJECT"}
+            clusterOptions = {"--clusters=genius --account=${params.vsc_kul_hasselt_tier2_project}"}
             beforeScript   = 'module load cluster/genius/superdome'
             // 6000 - 228 so 228GB for overhead, max is 5910888MB
             resourceLimits = [ memory: 5772.GB, cpus: 14, time: 168.h]