feat: Add nf-core resource allocation parameters

nextflow.config

@@ -17,8 +17,34 @@ params {
 }
 
 process {
-    errorStrategy = 'finish'
+    cpus = { check_max(1 * task.attempt, 'cpus') }
-    time = '7d'
+    memory = { check_max(6.GB * task.attempt, 'memory') }
+    time = { check_max(4.h * task.attempt, 'time') }
+
+    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
+    maxRetries = 1
+    maxErrors = '-1'
+
+    withLabel:process_single {
+        cpus = { check_max(1, 'cpus') }
+        memory = { check_max( 6.GB * task.attempt, 'memory') }
+        time = { check_max( 4.h * task.attempt, 'time') }
+    }
+    withLabel:process_low {
+        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 {
+        cpus = { check_max( 6 * task.attempt, 'cpus') }
+        memory = { check_max( 36.GB * task.attempt, 'memory') }
+        time = { check_max( 8.h * task.attempt, 'time') }
+    }
+    withLabel:process_high {
+        cpus = { check_max( 12 * task.attempt, 'cpus') }
+        memory = { check_max( 72.GB * task.attempt, 'memory') }
+        time = { check_max( 16.h  * task.attempt, 'time') }
+    }
 
     withName: 'HAPLINK_ML_HAPLOTYPES' {
         ext.ml_args = """
@@ -41,3 +67,34 @@ env {
     R_PROFILE_USER   = "/.Rprofile"
     R_ENVIRON_USER   = "/.Renviron"
 }
+
+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
+        }
+    }
+}